diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 9693 |
1 files changed, 5092 insertions, 4601 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4cbffac000..534204a16a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,16 +1,17 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr> -;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de> ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> +;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -72,7 +73,7 @@ `((upstream-name . "org.EcK12.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/org.EcK12.eg.db") (synopsis "Genome wide annotation for E coli strain K12") (description @@ -102,7 +103,7 @@ analysis.") (properties `((upstream-name . "org.Bt.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/org.Bt.eg.db") (synopsis "Genome wide annotation for Bovine") (description @@ -124,7 +125,7 @@ based on mapping using Entrez Gene identifiers.") (properties `((upstream-name . "reactome.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/reactome.db/") (synopsis "Annotation maps for reactome") (description @@ -147,7 +148,7 @@ database, assembled using data from REACTOME.") `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/") (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)") @@ -170,7 +171,7 @@ taurus (UCSC version bosTau8).") `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") (synopsis "Full genome sequences for Worm") @@ -195,7 +196,7 @@ objects.") `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") (synopsis "Full genome sequences for Worm") @@ -220,7 +221,7 @@ objects.") `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") (synopsis "Full genome sequences for Fly") @@ -245,7 +246,7 @@ objects.") `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") (synopsis "Full genome sequences for Fly") @@ -270,9 +271,7 @@ Biostrings objects.") `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-dmelanogaster-ucsc-dm3" - ,r-bsgenome-dmelanogaster-ucsc-dm3))) + (list r-bsgenome r-bsgenome-dmelanogaster-ucsc-dm3)) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") (synopsis "Full masked genome sequences for Fly") (description @@ -286,6 +285,28 @@ RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") (license license:artistic2.0))) +(define-public r-bsgenome-drerio-ucsc-danrer11 + (package + (name "r-bsgenome-drerio-ucsc-danrer11") + (version "1.4.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer11" + version 'annotation)) + (sha256 + (base32 "08a928mqzv2jxngjcs4yr6ni1b9z9al6jdngwi438j8hm41cwk4v")))) + (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11"))) + (build-system r-build-system) + (propagated-inputs + (list r-bsgenome)) + (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11") + (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)") + (description + "This package provides full genome sequences for Danio rerio (Zebrafish) +as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.") + (license license:artistic2.0))) + (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 (package (name "r-bsgenome-hsapiens-1000genomes-hs37d5") @@ -301,7 +322,7 @@ Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") (synopsis "Full genome sequences for Homo sapiens") @@ -324,7 +345,7 @@ Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) (build-system r-build-system) - (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) + (propagated-inputs (list r-bsgenome)) (home-page "https://bioconductor.org/packages/release/data/annotation/html/\ BSgenome.Hsapiens.NCBI.GRCh38.html") @@ -349,9 +370,7 @@ provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" - ,r-bsgenome-hsapiens-ucsc-hg19))) + (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19)) (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") (synopsis "Full masked genome sequences for Homo sapiens") (description @@ -380,7 +399,7 @@ default.") `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") (synopsis "Full genome sequences for Mouse") @@ -404,9 +423,7 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-mmusculus-ucsc-mm9" - ,r-bsgenome-mmusculus-ucsc-mm9))) + (list r-bsgenome r-bsgenome-mmusculus-ucsc-mm9)) (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") (synopsis "Full masked genome sequences for Mouse") (description @@ -435,7 +452,7 @@ default." ) `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") (synopsis "Full genome sequences for Mouse") @@ -478,7 +495,7 @@ ID and species. It is used by functions in the GenomeInfoDb package.") `((upstream-name . "GO.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/GO.db") (synopsis "Annotation maps describing the entire Gene Ontology") (description @@ -500,12 +517,12 @@ information about the latest version of the Gene Ontologies.") `((upstream-name . "Homo.sapiens"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-go-db" ,r-go-db) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) - ("r-organismdbi" ,r-organismdbi) - ("r-annotationdbi" ,r-annotationdbi))) + (list r-genomicfeatures + r-go-db + r-org-hs-eg-db + r-txdb-hsapiens-ucsc-hg19-knowngene + r-organismdbi + r-annotationdbi)) (home-page "https://bioconductor.org/packages/Homo.sapiens/") (synopsis "Annotation package for the Homo.sapiens object") (description @@ -527,13 +544,12 @@ several related annotation packages.") (properties `((upstream-name . "Mus.musculus"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-go-db" ,r-go-db) - ("r-org-mm-eg-db" ,r-org-mm-eg-db) - ("r-organismdbi" ,r-organismdbi) - ("r-txdb-mmusculus-ucsc-mm10-knowngene" - ,r-txdb-mmusculus-ucsc-mm10-knowngene))) + (list r-annotationdbi + r-genomicfeatures + r-go-db + r-org-mm-eg-db + r-organismdbi + r-txdb-mmusculus-ucsc-mm10-knowngene)) (home-page "https://bioconductor.org/packages/Mus.musculus") (synopsis "Annotation package for the Mus.musculus object") (description @@ -555,7 +571,7 @@ from several related annotation packages.") `((upstream-name . "org.Ce.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") (synopsis "Genome wide annotation for Worm") (description @@ -577,7 +593,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.") `((upstream-name . "org.Dm.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") (synopsis "Genome wide annotation for Fly") (description @@ -599,7 +615,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.") `((upstream-name . "org.Dr.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") (synopsis "Annotation for Zebrafish") (description @@ -610,18 +626,18 @@ based on mapping using Entrez Gene identifiers.") (define-public r-org-hs-eg-db (package (name "r-org-hs-eg-db") - (version "3.7.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) (sha256 (base32 - "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) + "0mnddv42ll0sc0zxf7hkgilslykbvfn7xgxg1g8qi57q2dmpwb6j")))) (properties `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") (synopsis "Genome wide annotation for Human") (description @@ -643,7 +659,7 @@ on mapping using Entrez Gene identifiers.") `((upstream-name . "org.Mm.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") (synopsis "Genome wide annotation for Mouse") (description @@ -666,7 +682,7 @@ annotations for the genome of the model mouse Mus musculus.") `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") (synopsis "Full genome sequences for Homo sapiens") @@ -690,7 +706,7 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.") `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") (synopsis "Full genome sequences for Homo sapiens") @@ -714,7 +730,7 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") `((upstream-name . "EnsDb.Hsapiens.v75"))) (build-system r-build-system) (propagated-inputs - `(("r-ensembldb" ,r-ensembldb))) + (list r-ensembldb)) (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") (synopsis "Ensembl based annotation package") (description @@ -737,8 +753,7 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicfeatures" ,r-genomicfeatures))) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene") (synopsis "Annotation package for TxDb object(s)") @@ -762,7 +777,7 @@ exposing these as TxDb objects.") `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures))) + (list r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") (synopsis "Annotation package for human genome in TxDb format") @@ -787,7 +802,7 @@ track. The database is exposed as a @code{TxDb} object.") `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures))) + (list r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") (synopsis "Annotation package for human genome in TxDb format") @@ -812,8 +827,7 @@ track. The database is exposed as a @code{TxDb} object.") `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi))) + (list r-genomicfeatures r-annotationdbi)) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") (synopsis "Annotation package for mouse genome in TxDb format") @@ -838,9 +852,7 @@ database is exposed as a @code{TxDb} object.") `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi))) + (list r-bsgenome r-genomicfeatures r-annotationdbi)) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") @@ -867,8 +879,7 @@ based on the knownGene track.") `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicfeatures" ,r-genomicfeatures))) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") (synopsis "Annotation package for C elegans TxDb objects") (description @@ -891,11 +902,8 @@ by exposing these as TxDb objects.") `((upstream-name . "FDb.InfiniumMethylation.hg19"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) + (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") (description @@ -919,7 +927,7 @@ annotations.") `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) (build-system r-build-system) (propagated-inputs - `(("r-minfi" ,r-minfi))) + (list r-minfi)) (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") (synopsis "Manifest for Illumina's EPIC methylation arrays") (description @@ -940,7 +948,7 @@ annotations.") `((upstream-name . "DO.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/DO.db/") (synopsis "Annotation maps describing the entire Disease Ontology") (description @@ -948,6 +956,26 @@ annotations.") Disease Ontology.") (license license:artistic2.0))) +(define-public r-hgu133plus2-db + (package + (name "r-hgu133plus2-db") + (version "3.13.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hgu133plus2.db" version 'annotation)) + (sha256 + (base32 "0i6cfk7ahql4fcgrq0dai9gkjbsahyzd9iv4lqv1ad58fzkmipnx")))) + (properties `((upstream-name . "hgu133plus2.db"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi r-org-hs-eg-db)) + (home-page "https://bioconductor.org/packages/hgu133plus2.db") + (synopsis "Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data") + (description + "This package provides Affymetrix HG-U133_Plus_2 array annotation +data (chip hgu133plus2) assembled using data from public repositories.") + (license license:artistic2.0))) + (define-public r-pfam-db (package (name "r-pfam-db") @@ -962,7 +990,7 @@ Disease Ontology.") (properties `((upstream-name . "PFAM.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/PFAM.db") (synopsis "Set of protein ID mappings for PFAM") (description @@ -986,12 +1014,12 @@ using data from public repositories.") `((upstream-name . "phastCons100way.UCSC.hg19"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicscores" ,r-genomicscores) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-bsgenome + r-genomeinfodb + r-genomicranges + r-genomicscores + r-iranges + r-s4vectors)) (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") (synopsis "UCSC phastCons conservation scores for hg19") (description @@ -1017,7 +1045,7 @@ species.") `((upstream-name . "ABAData"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/ABAData/") (synopsis "Gene expression in human brain regions from Allen Brain Atlas") (description @@ -1055,38 +1083,38 @@ All datasets are restricted to protein coding genes.") (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "0m6wphlriq7y21ih1p2kzml5jzcic79jc52kkk59dkjj8j88yllk")))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-aneufinderdata" ,r-aneufinderdata) - ("r-ecp" ,r-ecp) - ("r-foreach" ,r-foreach) - ("r-doparallel" ,r-doparallel) - ("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-bamsignals" ,r-bamsignals) - ("r-dnacopy" ,r-dnacopy) - ("r-biostrings" ,r-biostrings) - ("r-genomicalignments" ,r-genomicalignments) - ("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2) - ("r-ggdendro" ,r-ggdendro) - ("r-ggrepel" ,r-ggrepel) - ("r-reordercluster" ,r-reordercluster) - ("r-mclust" ,r-mclust) - ("r-cowplot" ,r-cowplot))) + "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0")))) + (build-system r-build-system) + (native-inputs + (list r-knitr)) + (propagated-inputs + (list r-genomicranges + r-aneufinderdata + r-ecp + r-foreach + r-doparallel + r-biocgenerics + r-s4vectors + r-genomeinfodb + r-iranges + r-rsamtools + r-bamsignals + r-dnacopy + r-biostrings + r-genomicalignments + r-ggplot2 + r-reshape2 + r-ggdendro + r-ggrepel + r-reordercluster + r-mclust + r-cowplot)) (home-page "https://bioconductor.org/packages/AneuFinder/") (synopsis "Copy number variation analysis in single-cell-sequencing data") (description "This package implements functions for copy number variant @@ -1129,10 +1157,8 @@ from Illumina 450k methylation arrays.") `((upstream-name . "biscuiteerData"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-curl" ,r-curl) - ("r-experimenthub" ,r-experimenthub))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-annotationhub r-curl r-experimenthub)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biscuiteerData") (synopsis "Data package for Biscuiteer") (description @@ -1140,6 +1166,35 @@ from Illumina 450k methylation arrays.") biscuiteer.") (license license:gpl3))) +(define-public r-celldex + (package + (name "r-celldex") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "celldex" version 'experiment)) + (sha256 + (base32 "04w60fx3s3wlirmr65nsz6d7ig48j9fzimdr8kbdqv1g80ivdcq1")))) + (properties `((upstream-name . "celldex"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-annotationhub + r-delayedarray + r-delayedmatrixstats + r-experimenthub + r-s4vectors + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/LTLA/celldex") + (synopsis "Reference index for cell types") + (description + "This package provides a collection of reference expression datasets with +curated cell type labels, for use in procedures like automated annotation of +single-cell data or deconvolution of bulk RNA-seq.") + (license license:gpl3))) + (define-public r-chromstardata (package (name "r-chromstardata") @@ -1160,6 +1215,34 @@ biscuiteer.") chromstaR package.") (license license:gpl3))) +(define-public r-chromvarmotifs + (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076") + (revision "1")) + (package + (name "r-chromvarmotifs") + (version (git-version "0.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/GreenleafLab/chromVARmotifs") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q")))) + (properties `((upstream-name . "chromVARmotifs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-tfbstools" ,r-tfbstools))) + (home-page "https://github.com/GreenleafLab/chromVARmotifs") + (synopsis "Stores motif collections for use with motifmatchr or chromVAR") + (description + "This package stores motif collections as lists of @dfn{position +frequency matrix} (PWMatrixList) objects provided by the @code{TFBSTools} +package for use in R with packages like @code{motifmatchr} or +@code{chromVAR}.") + (license license:expat)))) + (define-public r-copyhelper (package (name "r-copyhelper") @@ -1199,8 +1282,7 @@ GenomicRanges Bioconductor package.") `((upstream-name . "geneLenDataBase"))) (build-system r-build-system) (propagated-inputs - `(("r-rtracklayer" ,r-rtracklayer) - ("r-genomicfeatures" ,r-genomicfeatures))) + (list r-rtracklayer r-genomicfeatures)) (home-page "https://bioconductor.org/packages/geneLenDataBase/") (synopsis "Lengths of mRNA transcripts for a number of genomes") (description @@ -1225,7 +1307,7 @@ genomes and gene ID formats, largely based on the UCSC table browser.") ;; make sense to build substitutes. (arguments `(#:substitutable? #f)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Experimental data for use with the genomation package") (description @@ -1240,18 +1322,13 @@ downloaded from Encode.") (version "1.14.0") (source (origin (method url-fetch) - (uri (string-append - "http://bioconductor.org/packages/release/data/experiment" - "/src/contrib/pasilla_" version ".tar.gz")) + (uri (bioconductor-uri "pasilla" version 'experiment)) (sha256 (base32 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) (build-system r-build-system) (propagated-inputs - `(("r-biocstyle" ,r-biocstyle) - ("r-dexseq" ,r-dexseq) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown))) + (list r-biocstyle r-dexseq r-knitr r-rmarkdown)) (home-page "https://www.bioconductor.org/packages/pasilla/") (synopsis "Data package with per-exon and per-gene read counts") (description "This package provides per-exon and per-gene read counts @@ -1302,7 +1379,7 @@ resulting in a complete gene expression profile for each cell.") (properties `((upstream-name . "ALL"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase))) + (list r-biobase)) (home-page "https://bioconductor.org/packages/ALL") (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") (description @@ -1327,7 +1404,7 @@ the form of an @code{exprSet} object.") (properties `((upstream-name . "affydata"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy))) + (list r-affy)) (home-page "https://bioconductor.org/packages/affydata/") (synopsis "Affymetrix data for demonstration purposes") (description @@ -1377,12 +1454,12 @@ yeast are also included.") `((upstream-name . "curatedTCGAData"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-experimenthub" ,r-experimenthub) - ("r-hdf5array" ,r-hdf5array) - ("r-multiassayexperiment" ,r-multiassayexperiment) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-annotationhub + r-experimenthub + r-hdf5array + r-multiassayexperiment + r-s4vectors + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/curatedTCGAData/") (synopsis "Curated data from The Cancer Genome Atlas") (description @@ -1395,20 +1472,39 @@ harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment.") (license license:artistic2.0))) +(define-public r-tcgabiolinksgui-data + (package + (name "r-tcgabiolinksgui-data") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment)) + (sha256 + (base32 "08zmlvycq3jz1zy0715x9f21nf3465c51k7w2jq12sfbap36pmjm")))) + (properties `((upstream-name . "TCGAbiolinksGUI.data"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data") + (synopsis "Data for the TCGAbiolinksGUI package") + (description "This package provides supporting data for the +TCGAbiolinksGUI package.") + (license license:gpl3))) + ;;; Packages (define-public r-biocversion (package (name "r-biocversion") - (version "3.13.1") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "0rsw8g4g1pcjw1zbx8x17yd3drhxqk4sx3cy3ddzy5731hl6mbfi")))) + "0qwzkh2alw7xhjprh719la0lg1q38pmjbipy3s2fy79m4xy8y8ik")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -1421,13 +1517,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.38.0") + (version "0.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "1kv7lzmyki3hi771v01nml1v1hzz8pyhqqv0xcdzqy354mlgx4m6")))) + "0nr5x4r8f2krnfrxm7wrzgzr7nbljypi985cbwx5hxhn95zmfifh")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -1441,21 +1537,21 @@ packages.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "1xhirbjdw09cqm4xvysxqicvqjbahavwvs7shg4cb05gwyd2ha8g")))) + "0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as")))) (build-system r-build-system) (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicalignments" ,r-genomicalignments) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rsamtools" ,r-rsamtools))) + (list r-s4vectors + r-iranges + r-genomicranges + r-genomicalignments + r-rtracklayer + r-rsamtools)) (home-page "https://bioconductor.org/packages/CoverageView/") (synopsis "Coverage visualization package for R") (description "This package provides a framework for the visualization of @@ -1468,25 +1564,25 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1avvmvrmldbscc7xd6a6k22xjykbzafvqf87wh5z9rx3qlzswsjx")))) + "0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-fastcluster" ,r-fastcluster) - ("r-ggplot2" ,r-ggplot2) - ("r-gviz" ,r-gviz) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase + r-biocgenerics + r-fastcluster + r-ggplot2 + r-gviz + r-plyr + r-reshape2 + r-rsqlite + r-rtracklayer + r-s4vectors)) (home-page "https://bioconductor.org/packages/cummeRbund/") (synopsis "Analyze Cufflinks high-throughput sequencing data") (description "This package allows for persistent storage, access, @@ -1495,24 +1591,54 @@ data. In addition, provides numerous plotting functions for commonly used visualizations.") (license license:artistic2.0))) +(define-public r-dearseq + (package + (name "r-dearseq") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "dearseq" version)) + (sha256 + (base32 + "07vr27rv3z86ajd62c0ilvfgz9z35qsiwwi5pv4sygbhnnjwh3rc")))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 + r-kernsmooth + r-matrixstats + r-patchwork + r-pbapply + r-statmod + r-survey + r-kernsmooth)) + (home-page "https://github.com/borishejblum/dearseq") + (synopsis "DEA for RNA-seq data through a robust variance component test") + (description + "This is a package for Differential Expression Analysis of RNA-seq data. +It features a variance component score test accounting for data +heteroscedasticity through precision weights. Perform both gene-wise and gene +set analyses, and can deal with repeated or longitudinal data.") + (license license:gpl2))) + (define-public r-decipher (package (name "r-decipher") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "0mr7glkx2d37l9nszs52m0kycpm14vxl5gdp3z7i5j7yig1sw2nk")))) + "0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm")))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biostrings + r-dbi + r-iranges + r-rsqlite + r-s4vectors + r-xvector)) (home-page "https://www.bioconductor.org/packages/DECIPHER/") (synopsis "Tools for deciphering and managing biological sequences") (description "This package provides a toolset for deciphering and managing @@ -1522,25 +1648,25 @@ biological sequences.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "0zz56hf417m7bgg2g2wpbaik30pi6h2nam1n5bviqgdn4mv8n0bs")))) + "1wi6j6yb6i9fs9yszfywqz3w50mhl85dkfmr4w3phwvkf0xkn81w")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation) - ("r-vgam" ,r-vgam))) + (list r-biostrings + r-genomicranges + r-iranges + r-rhtslib + r-summarizedexperiment + r-variantannotation + r-vgam)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/gerstung-lab/deepSNV/") (synopsis "Detection of subclonal SNVs in deep sequencing data") (description @@ -1558,24 +1684,21 @@ bases such as COSMIC.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.18.0") + (version "0.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0w632262dqzcnvq9s6jvc7naz93dayx51fsv05s0zb6cjwygbqjr")))) + "1cm6zh01mvhiq7zrik7q3dmgxinyjz1nyg6rfj93kpkvcb5d4wpj")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics))) + (list r-biocgenerics r-s4vectors r-iranges r-matrix + r-matrixgenerics)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/DelayedArray") (synopsis "Delayed operations on array-like objects") (description @@ -1588,28 +1711,88 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), @code{Matrix} objects, and ordinary arrays and data frames.") (license license:artistic2.0))) +(define-public r-derfinderhelper + (package + (name "r-derfinderhelper") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "derfinderHelper" version)) + (sha256 + (base32 "06x0wy2wzpngak1pnrj2p0xzlx1nbcz0hs3p9q5ic6ib2rgwrh35")))) + (properties `((upstream-name . "derfinderHelper"))) + (build-system r-build-system) + (propagated-inputs + (list r-iranges r-matrix r-s4vectors)) + (native-inputs + (list r-knitr)) + (home-page "https://github.com/leekgroup/derfinderHelper") + (synopsis "Helper for derfinder") + (description + "This package speeds up the derfinder package when using multiple cores. +It is particularly useful when using BiocParallel and it helps reduce the time +spent loading the full derfinder package when running the F-statistics +calculation in parallel.") + (license license:artistic2.0))) + +(define-public r-drimseq + (package + (name "r-drimseq") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DRIMSeq" version)) + (sha256 + (base32 "0y2jb0hb633id038zmwnfny6h4ai77fdyy02f77vha1z8xg5nl02")))) + (properties `((upstream-name . "DRIMSeq"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biocparallel + r-edger + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-mass + r-reshape2 + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/DRIMSeq") + (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq") + (description + "The package provides two frameworks. One for the differential +transcript usage analysis between different conditions and one for the tuQTL +analysis. Both are based on modeling the counts of genomic features (i.e., +transcripts) with the Dirichlet-multinomial distribution. The package also +makes available functions for visualization and exploration of the data and +results.") + (license license:gpl3+))) + (define-public r-bluster (package (name "r-bluster") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "128zd5vwlhmrkq0bpp1dxnkrcqfz1mjmdjlla4wqbjv7v6yyn6lg")))) + "1j24l12i3aga4qd827sj8b160yvrhlznggb4piddkmhjc0sppbjm")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs - `(("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-cluster" ,r-cluster) - ("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocneighbors + r-biocparallel + r-cluster + r-igraph + r-matrix + r-rcpp + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/bluster") (synopsis "Clustering algorithms for Bioconductor") (description"This package wraps common clustering algorithms in an easily @@ -1621,21 +1804,21 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "17sx0v5lq2zmg098ps4ksj1h0yla3vlh6s2w1ahqsq0nvm193scm")))) + "0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-genomeinfodb" ,r-genomeinfodb))) + (list r-biobase + r-iranges + r-genomicranges + r-rcolorbrewer + r-rtracklayer + r-genomeinfodb)) (home-page "https://bioconductor.org/packages/IdeoViz/") (synopsis "Plots data along a chromosomal ideogram") (description "This package provides functions to plot data associated with @@ -1645,19 +1828,18 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-iranges (package (name "r-iranges") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0dzj8wqbjzilh2dsaj3ylx958xqrv0c688ayfq2r1z7rs75qy7kx")))) + "07zs231wbfwwc1c1165rhp711fbss40p9l8kyjjv9flzpr3hr1pg")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-s4vectors)) (home-page "https://bioconductor.org/packages/IRanges") (synopsis "Infrastructure for manipulating intervals on sequences") (description @@ -1671,6 +1853,59 @@ naming and share the same rich and consistent \"Vector API\" as much as possible.") (license license:artistic2.0))) +(define-public r-isoformswitchanalyzer + (package + (name "r-isoformswitchanalyzer") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) + (sha256 + (base32 "14bqf39gw5ab5r9sr3afkig1jbzdvds1bmcvc6bpb45kschx7fwf")))) + (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-biostrings + r-bsgenome + r-dbi + r-dexseq + r-dplyr + r-drimseq + r-edger + r-futile-logger + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-limma + r-magrittr + r-plyr + r-rcolorbrewer + r-rcurl + r-readr + r-reshape2 + r-rtracklayer + r-stringr + r-tibble + r-tximeta + r-tximport + r-venndiagram + r-xvector)) + (native-inputs + (list r-knitr)) + (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/") + (synopsis "Analyze alternative splicing in RNA-seq data") + (description + "This is a package for the analysis of alternative splicing and isoform +switches with predicted functional consequences (e.g. gain/loss of protein +domains etc.) from quantification of all types of RNASeq by tools such as +Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.") + (license license:gpl2+))) + ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor. (define-public r-absfiltergsea (package @@ -1685,11 +1920,7 @@ possible.") (properties `((upstream-name . "AbsFilterGSEA"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq" ,r-deseq) - ("r-limma" ,r-limma) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") (synopsis "Improved false positive control of gene-permuting with absolute filtering") (description @@ -1713,10 +1944,9 @@ absolute GSEA.") (properties `((upstream-name . "BisqueRNA"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limsolve" ,r-limsolve))) + (list r-biobase r-limsolve)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.biorxiv.org/content/10.1101/669911v1") (synopsis "Decomposition of bulk expression with single-cell sequencing") (description "This package provides tools to accurately estimate cell type @@ -1743,10 +1973,8 @@ relative abundances across samples.") `((upstream-name . "deconstructSigs"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-reshape2" ,r-reshape2))) + (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb + r-reshape2)) (home-page "https://github.com/raerose01/deconstructSigs") (synopsis "Identifies signatures present in a tumor sample") (description "This package takes sample information in the form of the @@ -1756,6 +1984,33 @@ closely reconstructs the mutational profile.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on Bioconductor packages. +(define-public r-jetset + (package + (name "r-jetset") + (version "3.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "jetset" version)) + (sha256 + (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp")))) + (properties `((upstream-name . "jetset"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi r-org-hs-eg-db)) + (home-page "http://www.cbs.dtu.dk/biotools/jetset/") + (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays") + (description + "This package provides a one-to-one mapping from gene to \"best\" probe +set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a, +hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single +gene may be measured by multiple probe sets. This can present a mild +conundrum when attempting to evaluate a gene \"signature\" that is defined by +gene names rather than by specific probe sets. This package also includes the +pre-calculated probe set quality scores that were used to define the +mapping.") + (license license:artistic2.0))) + +;; This is a CRAN package, but it depends on Bioconductor packages. (define-public r-nmf (package (name "r-nmf") @@ -1770,25 +2025,25 @@ closely reconstructs the mutational profile.") (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-bigmemory" ,r-bigmemory) ; suggested - ("r-synchronicity" ,r-synchronicity) ; suggested - ("r-colorspace" ,r-colorspace) - ("r-digest" ,r-digest) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-gridbase" ,r-gridbase) - ("r-pkgmaker" ,r-pkgmaker) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-registry" ,r-registry) - ("r-reshape2" ,r-reshape2) - ("r-rngtools" ,r-rngtools) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-cluster + r-biobase + r-biocmanager + r-bigmemory ; suggested + r-synchronicity ; suggested + r-colorspace + r-digest + r-doparallel + r-foreach + r-ggplot2 + r-gridbase + r-pkgmaker + r-rcolorbrewer + r-registry + r-reshape2 + r-rngtools + r-stringr)) + (native-inputs + (list r-knitr)) (home-page "http://renozao.github.io/NMF") (synopsis "Algorithms and framework for nonnegative matrix factorization") (description @@ -1803,24 +2058,24 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0vz5y92gqcm0qk57qlba85bk683lzdr7vkmxv109rq6i17vdkkrm")))) + "0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a")))) (build-system r-build-system) (propagated-inputs - `(("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-preprocesscore" ,r-preprocesscore) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-affyio + r-biobase + r-biocgenerics + r-biocmanager + r-preprocesscore + r-zlibbioc)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://bioconductor.org/packages/affy") (synopsis "Methods for affymetrix oligonucleotide arrays") (description @@ -1831,17 +2086,17 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "07my5scdh6h0y1bx1h9y5m4fa8bnmw389f83gkb7cf19w4vp36b2")))) + "0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/affycomp/") (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") (description @@ -1852,21 +2107,19 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "1xwz22wf2smsvmd0d5lfadbsgscnl3fl9msypy2mml38k048p6vj")))) + "1qlfh1gcwa6akd5dhdqh260yaw1j6dap6a15ghwf74rchi5218sg")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-rcurl" ,r-rcurl) - ("r-xml" ,r-xml))) + (list r-biostrings r-rcurl r-xml)) (home-page "https://bioconductor.org/packages/AffyCompatible/") (synopsis "Work with Affymetrix GeneChip files") (description @@ -1880,20 +2133,18 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "0242ga68wrdk1kcmxfdbq73a0d3zhrzdlzkzphfg3q0zjbvg49jj")))) + "1vw3nxg9jvlw0zg9h70w2ww8l42qpyvgf12hsla9hyyfhj3m6i9f")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-affydata" ,r-affydata) - ("r-biobase" ,r-biobase))) + (list r-affy r-affydata r-biobase)) (home-page "https://bioconductor.org/packages/affyContam/") (synopsis "Structured corruption of Affymetrix CEL file data") (description @@ -1905,38 +2156,38 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "1dx861spr3kn1dxwhf43s5l1r7bmrq0h6538l3q64iiwzzc6krdh")))) + "1ccyaj129ii9f47r41qsy34y6ck4wna55j8vz3v3hbldddn93f40")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-edger" ,r-edger) - ("r-gcrma" ,r-gcrma) - ("r-glimma" ,r-glimma) - ("r-ggplot2" ,r-ggplot2) - ("r-gostats" ,r-gostats) - ("r-gplots" ,r-gplots) - ("r-hwriter" ,r-hwriter) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-oligoclasses" ,r-oligoclasses) - ("r-reportingtools" ,r-reportingtools) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xtable" ,r-xtable))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-affy + r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-edger + r-gcrma + r-glimma + r-ggplot2 + r-gostats + r-gplots + r-hwriter + r-lattice + r-limma + r-oligoclasses + r-reportingtools + r-rsqlite + r-s4vectors + r-xtable)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/affycoretools/") (synopsis "Functions for analyses with Affymetrix GeneChips") (description @@ -1947,19 +2198,19 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "07kibqsm888g06qqqa4648ph877kriy74kprbri8nyx83y8aspjr")))) + "02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm")))) (build-system r-build-system) (propagated-inputs - `(("r-zlibbioc" ,r-zlibbioc))) + (list r-zlibbioc)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/bmbolstad/affyio") (synopsis "Tools for parsing Affymetrix data files") (description @@ -1971,14 +2222,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.64.1") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "0lr0kmp087j2g4i5kd7rh8a038ymp6z82861lyql2fwk5dh80043")))) + "1bd0f8ifj6l7dx2m3wpmd0mji2gdf39mzgcjf9lbvvmbqnbxbcal")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -1999,23 +2250,23 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "13ny596wh65sw7dbw0zd4h84d6k1w99g91c4sqy83mdzgpv73sz7")))) + "0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-httr" ,r-httr) - ("r-xml" ,r-xml) - ("r-xtable" ,r-xtable))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-httr + r-xml + r-xtable)) (home-page "https://bioconductor.org/packages/annotate") (synopsis "Annotation for microarrays") @@ -2026,26 +2277,26 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.54.1") + (version "1.56.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0fcammls431pgmp47r85k0zh3bz42bajbqdmafd31kpqncc1ijal")))) + "01zwq14msbbwzxv8rgpmyr74ymvhq0vnmxkxxwd886iac5vjlgi8")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-keggrest" ,r-keggrest) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase + r-biocgenerics + r-dbi + r-keggrest + r-iranges + r-rsqlite + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/AnnotationDbi") (synopsis "Annotation database interface") (description @@ -2056,21 +2307,20 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "0799jja6v7l3jsi26wbjalkr5lriaxid05xb5g36iq93myhaj0sa")))) + "15fp1228yb06jm5cblvhw3qv9mlpbjfggaz2nvi3p46mby1vs64w")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-lazyeval" ,r-lazyeval))) + (list r-genomicranges r-lazyeval)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Bioconductor/AnnotationFilter") (synopsis "Facilities for filtering Bioconductor annotation resources") (description @@ -2082,28 +2332,28 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "1by3diy0y4809k97cw97mp4j177gn1dzhqil8myij1r7b8sk7hax")))) + "02wvni5q560idi6677g5f4md73z4qzjl5yycxv5dbvgbl2picisz")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-rcurl + r-rsqlite + r-s4vectors + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/AnnotationForge") (synopsis "Code for building annotation database packages") (description @@ -2114,32 +2364,32 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.0.1") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "12i8lafy1z97gs4knqi7r5l1hd7dr6j8a23qj4fkdpqsdpyz21z7")))) + "0ks8yzvvs2r66pb9687mkskf0n3wgvp7h92k83b0a1q32sca5wng")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biocversion" ,r-biocversion) - ("r-curl" ,r-curl) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-interactivedisplaybase" ,r-interactivedisplaybase) - ("r-rappdirs" ,r-rappdirs) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocfilecache + r-biocgenerics + r-biocmanager + r-biocversion + r-curl + r-dplyr + r-httr + r-interactivedisplaybase + r-rappdirs + r-rsqlite + r-s4vectors + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/AnnotationHub") (synopsis "Client to access AnnotationHub resources") (description @@ -2155,21 +2405,18 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.22.0") + (version "3.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "1yvq6l1p8cpijvlib4fn9y88ihn0gaalrmgx82jgrfmnszkqn3y5")))) + "12qa85hsp8d1xhgn27iymknbhpnp9bd7hsgqxwvp1i8kki06z5hp")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs - `(("r-matrixstats" ,r-matrixstats) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) + (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/aroma.light") (synopsis "Methods for normalization and visualization of microarray data") (description @@ -2182,24 +2429,24 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "1ljrip0jlxjcljqac7vzvwqbcqil5v4f4s4bhpq4akvdkshas6mn")))) + "03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-biocgenerics + r-genomicranges + r-iranges + r-rcpp + r-rhtslib + r-zlibbioc)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/bamsignals") (synopsis "Extract read count signals from bam files") (description @@ -2212,18 +2459,18 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1sg8w8860zhlz9s1pf75xa8asd2hyqsj13fh5xc37hf5yqdfkavr")))) + "0kar2kgaayp5l7xv9zcxj61l01m8jlwnppql6qf01wsz36dacgww")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) + (list r-biocgenerics)) (home-page "https://bioconductor.org/packages/Biobase") (synopsis "Base functions for Bioconductor") (description @@ -2234,28 +2481,28 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.48.3") + (version "2.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "096s243yzbhhz3wsm7azml5sznqczmcpi5g0gnb02mah1przczfx")))) + "1lm8axjmi2k1d2x0gdlvs0fzsd68xvxx7sn1wn6v4wr0pv85qhkz")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-progress" ,r-progress) - ("r-rappdirs" ,r-rappdirs) - ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2))) + (list r-annotationdbi + r-biocfilecache + r-digest + r-httr + r-progress + r-rappdirs + r-stringr + r-xml + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/biomaRt") (synopsis "Interface to BioMart databases") (description @@ -2272,13 +2519,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.26.2") + (version "1.28.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1y459cygq21f3igsdlxz1zlyad8qbl2qlr5h2d2dpnvblykvf48i")))) + "0lkp7m2l66zq8yl788mkvi9kpb1haywxpf6ip9xl5y6iwm1w2b8p")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -2306,16 +2553,14 @@ powerful online queries from gene annotation to database mining.") (("\\today") "later")) ;; Initialize the random number generator seed when building. - (substitute* "R/internal_rng_stream.R" + (substitute* "R/rng.R" (("\"L'Ecuyer-CMRG\"\\)" m) (string-append m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) (propagated-inputs - `(("r-futile-logger" ,r-futile-logger) - ("r-snow" ,r-snow) - ("r-bh" ,r-bh))) + (list r-futile-logger r-snow r-bh)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocParallel") (synopsis "Bioconductor facilities for parallel evaluation") (description @@ -2327,23 +2572,23 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.60.2") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0ai0fg0w4l0a7avbafdbqjgjpg91myxalwrg2i3ixm1l2lyyfyah")))) + "11qkw863mkfz3mc55v2gmfr4w3xziqfb5pq3hmjqpn8vpw8ax3xq")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-crayon" ,r-crayon) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics + r-crayon + r-genomeinfodb + r-iranges + r-s4vectors + r-xvector)) (home-page "https://bioconductor.org/packages/Biostrings") (synopsis "String objects and algorithms for biological sequences") (description @@ -2355,36 +2600,36 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "14jyyg3ggdhaqhp0j4qf6dapykh76fygbaa4lr7czqbc5mr0iw23")))) + "0kg71p7sqfvxal0c19zrws1ffaqgyi8p605l3z6mkq5ldi26pajz")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dichromat" ,r-dichromat) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) + (list r-annotationdbi + r-annotationfilter + r-biocgenerics + r-biostrings + r-dichromat + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-hmisc + r-iranges + r-rcolorbrewer + r-rlang + r-rsamtools + r-s4vectors + r-scales + r-summarizedexperiment + r-variantannotation)) (home-page "https://bioconductor.org/packages/biovizBase") (synopsis "Basic graphic utilities for visualization of genomic data") (description @@ -2397,27 +2642,27 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1jhissp9ad1rn2p0bzr3yslbn84yqbaqgnn5p9hyacwr7mr091cn")))) + "1b023dpy8ygq0kd6qy0mk97c66gzpf39y2s0n89kmv61z5sg0jyi")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-matrixstats + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector)) (home-page "https://bioconductor.org/packages/BSgenome") (synopsis "Infrastructure for Biostrings-based genome data packages") (description @@ -2428,27 +2673,27 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0f76pb7h8qc51mca5pq00m9p02sbkcj6ywfzli20qai2ykpfr71x")))) + "164zp4la9rqnp5vpn2y2p6plc5yxyk2kmn0z3d2flla54zc1b427")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-graph" ,r-graph) - ("r-gseabase" ,r-gseabase) - ("r-matrix" ,r-matrix) - ("r-rbgl" ,r-rbgl) - ("r-dbi" ,r-dbi))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-genefilter + r-graph + r-gseabase + r-matrix + r-rbgl + r-dbi)) (home-page "https://bioconductor.org/packages/Category") (synopsis "Category analysis") (description @@ -2459,37 +2704,36 @@ analysis.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.28.3") + (version "1.30.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "18hdgml80770c0xgd06zrl8px1ql9fa65rirfkq07z7rzpnd23rw")))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-boot" ,r-boot) - ("r-enrichplot" ,r-enrichplot) - ("r-iranges" ,r-iranges) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-ggplot2" ,r-ggplot2) - ("r-gplots" ,r-gplots) - ("r-gtools" ,r-gtools) - ("r-dplyr" ,r-dplyr) - ("r-plotrix" ,r-plotrix) - ("r-dplyr" ,r-dplyr) - ("r-magrittr" ,r-magrittr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" - ,r-txdb-hsapiens-ucsc-hg19-knowngene))) + "1f9m1p1viiigkmv15r2mknjrfw047jw1fylpqz5ipigc3jrphj1g")))) + (build-system r-build-system) + (native-inputs + (list r-knitr)) + (propagated-inputs + (list r-annotationdbi + r-biocgenerics + r-boot + r-enrichplot + r-iranges + r-genomeinfodb + r-genomicranges + r-genomicfeatures + r-ggplot2 + r-gplots + r-gtools + r-dplyr + r-plotrix + r-dplyr + r-magrittr + r-rcolorbrewer + r-rtracklayer + r-s4vectors + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://www.bioconductor.org/packages/ChIPseeker/") (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization") (description "This package implements functions to retrieve the nearest @@ -2506,22 +2750,22 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "078p9h0zghlhpd6cr54nww1mk7q97imx8yqfayw5m2yq4097ivbi")))) + "1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread))) + (list r-biocgenerics + r-genomicranges + r-iranges + r-lattice + r-s4vectors + r-shortread)) (home-page "https://bioconductor.org/packages/chipseq") (synopsis "Package for analyzing ChIPseq data") (description @@ -2532,33 +2776,32 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "0jl96msj1njdrvngg68s50vmphvhi2lfwlv34x07pcdzgkjjs41f")))) + "124w74mk0zk035wyr7cimblzx5blags4n5c8f83mp7iimxcb4gcn")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) (propagated-inputs - `(("r-cairo" ,r-cairo) - ("r-circlize" ,r-circlize) - ("r-clue" ,r-clue) - ("r-colorspace" ,r-colorspace) - ("r-digest" ,r-digest) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-getoptlong" ,r-getoptlong) - ("r-globaloptions" ,r-globaloptions) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-circlize + r-clue + r-colorspace + r-digest + r-doparallel + r-foreach + r-getoptlong + r-globaloptions + r-iranges + r-matrixstats + r-png + r-rcolorbrewer)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/jokergoo/ComplexHeatmap") (synopsis "Making Complex Heatmaps") @@ -2572,31 +2815,31 @@ self-defined annotation graphics.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0pacs714d9b1fdz68pp9ca0x77d376s19lxb82np4l9fgx0rgkxp")))) + "0xm5gjzi4r1xzyn7r669blqxhyhmbk9rh9k2gn696j14hbhc1hcy")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-chipseq" ,r-chipseq) - ("r-copyhelper" ,r-copyhelper) - ("r-data-table" ,r-data-table) - ("r-dnacopy" ,r-dnacopy) - ("r-futile-logger" ,r-futile-logger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocparallel + r-chipseq + r-copyhelper + r-data-table + r-dnacopy + r-futile-logger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-gtools + r-iranges + r-matrixstats + r-rsamtools + r-s4vectors)) (home-page "https://github.com/PeeperLab/CopywriteR") (synopsis "Copy number information from targeted sequencing") (description @@ -2623,14 +2866,14 @@ number detection tools.") (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-lattice" ,r-lattice) - ("r-locfit" ,r-locfit) - ("r-mass" ,r-mass) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-biobase + r-biocgenerics + r-genefilter + r-geneplotter + r-lattice + r-locfit + r-mass + r-rcolorbrewer)) (home-page "https://www-huber.embl.de/users/anders/DESeq/") (synopsis "Differential gene expression analysis") (description @@ -2643,32 +2886,32 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0r1brwmj7av0bj72jajn27vx3zs1bgg8qfbhf02fln6kf7im4kaz")))) + "0whk29zrmv9mrlc4w5ghy0fd29v8hfr8jccwgrn59mf3mkmfb2b9")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-genefilter + r-geneplotter + r-genomicranges + r-ggplot2 + r-iranges + r-locfit + r-rcpp + r-rcpparmadillo + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/DESeq2") (synopsis "Differential gene expression analysis") (description @@ -2681,36 +2924,36 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1zywh30f4j4rj0f9w6yk5xr9mvdbg8gicy3wsb8yxdnamadyr7x4")))) + "1wd4bjd0a53s689yvb2lxzdiy0synh6ncfcly3cfw37kpdj8lds1")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biomart" ,r-biomart) - ("r-deseq2" ,r-deseq2) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-statmod" ,r-statmod) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biomart + r-deseq2 + r-genefilter + r-geneplotter + r-genomicranges + r-hwriter + r-iranges + r-rcolorbrewer + r-rsamtools + r-s4vectors + r-statmod + r-stringr + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/DEXSeq") (synopsis "Inference of differential exon usage in RNA-Seq") (description @@ -2726,23 +2969,21 @@ exploration of the results.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "0ikmj0300lfzj6q1vyahfyx5kwi5h59mds7ym4f2j1bbxqzy6ssl")))) + "06nallp9jj2vmaa7d18g6hiymjc109szdv8sp51r87n7s38bvyq6")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) + (list gsl)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-iranges r-s4vectors)) (home-page "https://bioconductor.org/packages/DirichletMultinomial") (synopsis "Dirichlet-Multinomial mixture models for microbiome data") (description @@ -2755,31 +2996,31 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-edaseq (package (name "r-edaseq") - (version "2.26.1") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "0pakcbkalhhqz3d9lpfx3hscf53k24mlmrywxxzfg43yq57srkql")))) + "1vygfdxbjcww7sqzc3j7sp7w13dx10vlzy9z31flf7345qp6blj7")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-aroma-light" ,r-aroma-light) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-aroma-light + r-biobase + r-biocgenerics + r-biocmanager + r-biomart + r-biostrings + r-genomicfeatures + r-genomicranges + r-iranges + r-rsamtools + r-shortread)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/drisso/EDASeq") (synopsis "Exploratory data analysis and normalization for RNA-Seq") (description @@ -2795,20 +3036,17 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.34.1") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0f6apsjq6cn794840ls9y2n0hix1gyhvkdgxch1v22qr4sq0c86k")))) + "1d18kdfi9vjhhw5kwfy5airrd3c16fh4wbwppbhwgawm038mwavk")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-statmod" ,r-statmod))) ;for estimateDisp + (list r-limma r-locfit r-rcpp r-statmod)) ;for estimateDisp (home-page "http://bioinf.wehi.edu.au/edgeR") (synopsis "EdgeR does empirical analysis of digital gene expression data") (description "This package can do differential expression analysis of @@ -2823,34 +3061,34 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.16.4") + (version "2.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "15yllkxr6sj5pfvkvv285nk3q5374nzq1iz8ywmnrq910k3xagd8")))) + "0q56gv0isa9ayw505py7i7x65pvcshmd2j1mna1wpbk66wqj4qzx")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-protgenerics" ,r-protgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationdbi + r-annotationfilter + r-biobase + r-biocgenerics + r-biostrings + r-curl + r-dbi + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-protgenerics + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jotsetung/ensembldb") (synopsis "Utilities to create and use Ensembl-based annotation databases") (description @@ -2868,21 +3106,18 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "006v7qs707xmnr35b7rw135pyvacrmhv55a3c53birkpsrjgkps0")))) + "1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase r-biocgenerics r-genomicranges r-iranges + r-s4vectors)) (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") (synopsis "Fast segmentation algorithm for genetic sequencing data") (description @@ -2898,20 +3133,17 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "0z7hrwdm6my6p7z04bcpfhqk72pd0s1bdzvsiiym59qj79fbvb83")))) + "1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-keggrest" ,r-keggrest))) + (list r-annotationdbi r-go-db r-graph r-keggrest)) (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" "articles/10.1186/1471-2105-10-161")) (synopsis "Generally applicable gene-set enrichment for pathway analysis") @@ -2929,24 +3161,20 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0dy9pmlb0pc9b4ks5fb9zgnmhc9f2mkqmsdlb7f5z88xmj68y4qk")))) + "05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + (list gfortran r-knitr)) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-survival" ,r-survival))) + (list r-annotate r-annotationdbi r-biobase r-biocgenerics + r-survival)) (home-page "https://bioconductor.org/packages/genefilter") (synopsis "Filter genes from high-throughput experiments") (description @@ -2957,17 +3185,16 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "1kfw3h68rvbafhklds6sfmviwv91nms8wk0ywzkjg5h3mmgxbsv9")))) + "18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm")))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-gplots" ,r-gplots))) + (list r-rcolorbrewer r-gplots)) (home-page "https://www.bioconductor.org/packages/GeneOverlap/") (synopsis "Test and visualize gene overlaps") (description "This package can be used to test two sets of gene lists @@ -2977,37 +3204,37 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0qa3b4mfd7l1sy4pw64zr2d90y5apah900krxjl4x39acygg0i2r")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-data-table" ,r-data-table) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridbase" ,r-gridbase) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-plotrix" ,r-plotrix) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqpattern" ,r-seqpattern))) - (native-inputs - `(("r-knitr" ,r-knitr))) + "0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j")))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-bsgenome + r-data-table + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gridbase + r-impute + r-iranges + r-matrixstats + r-plotrix + r-plyr + r-rcpp + r-readr + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-seqpattern)) + (native-inputs + (list r-knitr)) (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Summary, annotation and visualization of genomic data") (description @@ -3024,24 +3251,21 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.28.4") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0fjpgvpvyvl8cqgh2annib6h0c5li3aqz1ajfh5z5k5d0avdm4w0")))) + "1r0wblz9w4hqxm15wdssz0invx7hxhg3bnblkia6w3aazh30s6ns")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodbdata" ,r-genomeinfodbdata) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomeInfoDb") (synopsis "Utilities for manipulating chromosome identifiers") (description @@ -3054,26 +3278,26 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "00rq110jkh89nxgk05zh8kssxk8mb4dq0wjg3n7ivfmmm9wdwhp2")))) + "1jwksis94mk8bmdggk0w3kvxqwp4di6x78xgsjk6ij54710adyq9")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-s4vectors + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/GenomicAlignments") (synopsis "Representation and manipulation of short genomic alignments") (description @@ -3087,34 +3311,34 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.44.2") + (version "1.46.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "091p8xnf2xkqhind81vyv1rmy2fz2b3qalcbrsw4qnp24vgdv2am")))) + "0a3shdzc1r0f12q9w679hgj8ywrwbg36z7k0yp47dgfjl14lachk")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocio" ,r-biocio) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocio + r-biomart + r-biostrings + r-dbi + r-genomeinfodb + r-genomicranges + r-iranges + r-rcurl + r-rsqlite + r-rtracklayer + r-s4vectors + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomicFeatures") (synopsis "Tools for working with transcript centric annotations") (description @@ -3131,29 +3355,29 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "1plh14m7w6calw5yxcxp7g4bg8q00ax85m517wap78bni975k13y")))) + "0i5y6dk6z18yqj5k4zy756c6l57z9jq2w5a5dksh2di4qgdgjx3x")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-matrixgenerics + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation)) (home-page "https://bioconductor.org/packages/GenomicFiles") (synopsis "Distributed computing by file or by range") (description @@ -3165,24 +3389,20 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.44.0") + (version "1.46.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "1qxc6dcwdlkan3hg0j9yfhz7gyi9qg671yj6zizsk6mzl7qqva0x")))) + "133r27wsdyppjv9kq0d2xamx007lkf416nnlaygs4hs3a76p9xwx")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomicRanges") (synopsis "Representation and manipulation of genomic intervals") (description @@ -3196,26 +3416,26 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-gostats (package (name "r-gostats") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "0jjswy6qmfgr2f6vk3y9pdvs9x91gn31h55qllgh0qb2cb26g9wa")))) + "1f8wqdl0swnvs59i6ljjcaglfqv314n8zxy4crpx806gbjzpn76z")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-annotationforge" ,r-annotationforge) - ("r-biobase" ,r-biobase) - ("r-category" ,r-category) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rbgl" ,r-rbgl))) + (list r-annotate + r-annotationdbi + r-annotationforge + r-biobase + r-category + r-go-db + r-graph + r-rgraphviz + r-rbgl)) (home-page "https://bioconductor.org/packages/GOstats") (synopsis "Tools for manipulating GO and microarrays") (description @@ -3227,25 +3447,25 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0946kkykms79mqnx262q20xzrrhv7cv723xh378335ff41qyf63n")))) + "1i8rryvagxk2pd8nl4a6yldwv82yx869nvv95jf8v00bna08f4d6")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-graph" ,r-graph) - ("r-xml" ,r-xml))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-graph + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GSEABase") (synopsis "Gene set enrichment data structures and methods") (description @@ -3256,17 +3476,17 @@ Enrichment Analysis} (GSEA).") (define-public r-hpar (package (name "r-hpar") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "0q5pp04rq2gsh1kibvp8bvjkqc1kb46qpnj6agqp2vyqhrrfrm99")))) + "1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") (description "This package provides a simple interface to and data from @@ -3276,26 +3496,24 @@ the Human Protein Atlas project.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "0acpgv98529ic2i2k03knz05akb6h51wbz7sr5zgi8gk4nmawrlf")))) + "0pwmzwjf6agfp3bq6w8s3piwmzwjdd474qd8zmbzrm772qbadfr4")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, ;; which makes R abort the build. (arguments '(#:configure-flags '("--no-staged-install"))) (propagated-inputs - `(("curl" ,curl) - ("zlib" ,zlib) ; packages using rhtslib need to link with zlib - ("r-zlibbioc" ,r-zlibbioc))) + (list curl zlib ; packages using rhtslib need to link with zlib + r-zlibbioc)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/nhayden/Rhtslib") (synopsis "High-throughput sequencing library as an R package") (description @@ -3307,15 +3525,15 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0pprkv25avxhllddcssvqvy3nibmqkfwaq4xnlhka7858gyiyd1k")))) + "0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5")))) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (build-system r-build-system) (home-page "https://bioconductor.org/packages/impute") (synopsis "Imputation for microarray data") @@ -3327,23 +3545,21 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "00rgrrmglslgb6j7whp0m5dlyl4436r647br05rrpv8cxrmbs2iv")))) + "1pi887192k1jifb4k3pf2jn5hcl1xmmy6vwl22r9njsprdyb3kab")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-dt" ,r-dt) - ("r-shiny" ,r-shiny))) + (list r-biocgenerics r-dt r-shiny)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/interactiveDisplayBase") (synopsis "Base package for web displays of Bioconductor objects") (description @@ -3354,22 +3570,20 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "15313d20v3ziyn52fhc6fbzcy1kxjkdx18124bxhdfd14f4aypcd")))) + "1np3i1k7rki9akh70156ggmid52yy0is9q5vd3s45ra7an0ap279")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-httr" ,r-httr) - ("r-png" ,r-png))) + (list r-biostrings r-httr r-png)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/KEGGREST") (synopsis "Client-side REST access to KEGG") (description @@ -3380,13 +3594,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-limma (package (name "r-limma") - (version "3.48.3") + (version "3.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0385ac0hvvml99krcgcpp6q7layjhzgp9xcxkcjrpfg5mjg1z4sx")))) + "05ypmax1s6y1nz42bxn61wxhzzw6185q633crzpdcbbz3dz4vgvy")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -3399,37 +3613,37 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "147nag4rz2xpjkkf8rmhja9k4ixjj1hsb0lq3lw7mw6q67zxsvf3")))) + "02px46h2ynprss7kwll3i0jz0clrdg0bys70jacd432xw34nm2sx")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-emdbook" ,r-emdbook) - ("r-fastseg" ,r-fastseg) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-limma" ,r-limma) - ("r-mclust" ,r-mclust) - ("r-mgcv" ,r-mgcv) - ("r-qvalue" ,r-qvalue) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-data-table + r-emdbook + r-fastseg + r-genomeinfodb + r-genomicranges + r-gtools + r-iranges + r-kernsmooth + r-limma + r-mclust + r-mgcv + r-qvalue + r-r-utils + r-rcpp + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-zlibbioc)) + (native-inputs + (list r-knitr)) ; for vignettes (home-page "https://github.com/al2na/methylKit") (synopsis "DNA methylation analysis from high-throughput bisulfite sequencing results") @@ -3457,12 +3671,12 @@ TAB-Seq.") (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-iranges" ,r-iranges) - ("r-seqlogo" ,r-seqlogo) - ("r-xvector" ,r-xvector))) + (list r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-iranges + r-seqlogo + r-xvector)) (home-page "https://bioconductor.org/packages/motifRG") (synopsis "Discover motifs in high throughput sequencing data") (description @@ -3473,41 +3687,42 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.2.0") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "0433i4xbz8hrfaj8fxgzps3x8dqrl5vgwzg7qmp4cy5sb1lw5wvs")))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ;; These two packages are suggested packages - ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggalluvial" ,r-ggalluvial) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-nmf" ,r-nmf) - ("r-pracma" ,r-pracma) - ("r-purrr" ,r-purrr) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-variantannotation" ,r-variantannotation))) + "1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl")))) + (build-system r-build-system) + (native-inputs + (list r-knitr)) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-bsgenome + ;; These two packages are suggested packages + r-bsgenome-hsapiens-1000genomes-hs37d5 + r-bsgenome-hsapiens-ucsc-hg19 + r-cowplot + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggalluvial + r-ggdendro + r-ggplot2 + r-iranges + r-magrittr + r-nmf + r-pracma + r-purrr + r-rcolorbrewer + r-s4vectors + r-stringr + r-tibble + r-tidyr + r-variantannotation)) (home-page "https://bioconductor.org/packages/MutationalPatterns/") (synopsis "Extract and visualize mutational patterns in genomic data") (description "This package provides an extensive toolset for the @@ -3518,41 +3733,41 @@ in SNV base substitution data.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.18.0") + (version "2.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1z7s17j6zgb70m0khyf9icqlnbnzlivca7vw7j0vxyw417ld9lkr")))) + "0ip614mdwisz2hlmyfgngysq1s3hajb88cgdmygfc8i6kyxjkjzl")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-digest" ,r-digest) - ("r-ggplot2" ,r-ggplot2) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-maldiquant" ,r-maldiquant) - ("r-mass" ,r-mass) - ("r-mscoreutils" ,r-mscoreutils) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-pcamethods" ,r-pcamethods) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-vsn" ,r-vsn) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-affy + r-biobase + r-biocgenerics + r-biocparallel + r-digest + r-ggplot2 + r-impute + r-iranges + r-lattice + r-maldiquant + r-mass + r-mscoreutils + r-mzid + r-mzr + r-pcamethods + r-plyr + r-protgenerics + r-rcpp + r-s4vectors + r-scales + r-vsn + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/lgatto/MSnbase") (synopsis "Base functions and classes for MS-based proteomics") (description @@ -3563,14 +3778,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0r3vgigf4fk0xzfg8gcvad01jdh0fysh6x22m9qy77x6glyrxcj2")))) + "0dks5h3vp9ly8x24px2rl5blqicxybpxjnxvg2p1bwq8zvjkm38p")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments @@ -3579,32 +3794,32 @@ of mass spectrometry based proteomics data.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocstyle" ,r-biocstyle) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-msnbase" ,r-msnbase) - ("r-msmstests" ,r-msmstests) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-protgenerics" ,r-protgenerics) - ("r-purrr" ,r-purrr) - ("r-r-cache" ,r-r-cache) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-runit" ,r-runit) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-xtable" ,r-xtable))) + (list r-annotationdbi + r-annotationhub + r-biobase + r-biocgenerics + r-biocstyle + r-biostrings + r-data-table + r-doparallel + r-dplyr + r-foreach + r-ggplot2 + r-iterators + r-msnbase + r-msmstests + r-mzid + r-mzr + r-protgenerics + r-purrr + r-r-cache + r-rcpp + r-reshape2 + r-rlang + r-runit + r-stringr + r-tibble + r-xtable)) (home-page "https://bioconductor.org/packages/MSnID") (synopsis "Utilities for LC-MSn proteomics identifications") (description @@ -3620,25 +3835,25 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "1wsy6frxa5602jqb1nlqv39mzgpid8wfyvb9m2jb6srv7p59rgys")))) + "0r001amd4m99cv0ixw38rpz0zv0xqb0qyvs16bz1i4a756391qri")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-xml" ,r-xml))) + (list r-doparallel + r-foreach + r-iterators + r-plyr + r-protgenerics + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/mzID") (synopsis "Parser for mzIdentML files") (description @@ -3651,14 +3866,14 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.26.1") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "0z4cz6lir9gwzy0hxwv03wv36fkkfdb97p9wv4af020k0zkp3ipr")) + "1azq0wjjy6n5xc721gjz6afm43ajz15b4p34vgsdjzwg9qn1vrs1")) (modules '((guix build utils))) (snippet '(begin @@ -3680,20 +3895,20 @@ specific parser.") -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) #t))))) (inputs - `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.26.1. - ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources - ("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-ncdf4" ,r-ncdf4) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list ;; Our default boost package won't work here, unfortunately, even with + ;; mzR version 2.28.0. + boost-for-mysql ; use this instead of the bundled boost sources + zlib)) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-ncdf4 + r-protgenerics + r-rcpp + r-rhdf5lib + r-zlibbioc)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/sneumann/mzR/") (synopsis "Parser for mass spectrometry data files") (description @@ -3708,28 +3923,28 @@ previously been used in XCMS.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0p8ccpdchdwci4kv9y07wdadzgms8nipvg6rm1rll35jcflnnkxi")))) + "0zp6x2iqhn9s3xp07yilnr6hn73acvkdai5xip4iiwjdlnfffj83")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-graph" ,r-graph) - ("r-iranges" ,r-iranges) - ("r-rbgl" ,r-rbgl) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocmanager + r-dbi + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-s4vectors)) (home-page "https://bioconductor.org/packages/OrganismDbi") (synopsis "Software to enable the smooth interfacing of database packages") (description "The package enables a simple unified interface to several @@ -3740,21 +3955,18 @@ the fact that each of these packages implements a select methods.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.84.0") + (version "1.86.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1ccqsxn487dy92c2d1iffh9917z4zq5ia92zv2h6pi00jjc6ymb5")))) + "1fj2v6sna4lbw7ar9h93y2g4pzylqqp7760ih425gcai7s19xdrg")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp))) + (list r-biobase r-biocgenerics r-mass r-rcpp)) (home-page "https://github.com/hredestig/pcamethods") (synopsis "Collection of PCA methods") (description @@ -3770,14 +3982,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "1c79k8nc28782w5gxi7pkm8jmddq1hdw6khs9kgsp8dyk60ak6fq")))) + "0x53pk7h47gjza1q5pz7jb1qqhwa9z2rr5fr61qc92zl3mqk57m0")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -3790,19 +4002,18 @@ proteomics packages.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0l40ibf8g5s4ay83s92l198jjqc5l09hcmxqcjrpifvp5pjf9yy5")))) + "0k2p1lwdvix4n742a97lv988rx5kg8cvcmzgyzj0538n1nz0lxk0")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-graph" ,r-graph))) + (list r-bh r-graph)) (home-page "https://www.bioconductor.org/packages/RBGL") (synopsis "Interface to the Boost graph library") (description @@ -3813,45 +4024,45 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "0l92v870ndna8zjqwzf22fb9vyhkh6942v4gaiqr1yc4qr521p5p")))) + "02zwz7c8ljmdcfxj54xns0a31sj616x63q63wxhxa1nb4dhgmvk7")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggseqlogo" ,r-ggseqlogo) - ("r-gprofiler2" ,r-gprofiler2) - ("r-iranges" ,r-iranges) - ("r-knitr" ,r-knitr) - ("r-pbapply" ,r-pbapply) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-plotrix" ,r-plotrix) - ("r-proxy" ,r-proxy) - ("r-ranger" ,r-ranger) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-s4vectors" ,r-s4vectors) - ("pandoc" ,pandoc))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-cowplot + r-data-table + r-dt + r-genomation + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-gprofiler2 + r-iranges + r-knitr + r-pbapply + r-pheatmap + r-plotly + r-plotrix + r-proxy + r-ranger + r-rsqlite + r-rtracklayer + r-rmarkdown + r-s4vectors + pandoc)) + (native-inputs + (list r-knitr)) (synopsis "RNA-centric annotation system") (description "RCAS aims to be a standalone RNA-centric annotation system that provides @@ -3863,27 +4074,27 @@ library implementing most of the pipeline's features.") (define-public r-regioner (package (name "r-regioner") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0xzzaz3cl6pyxfsg0d931v8k15wbd05s5mnsb7igxldc5qqg3nsl")))) + "0y1mawzfvxrympc47q3isk96sl9d1bc8kdsxpm8rnhqg5bmgwya6")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-memoise" ,r-memoise) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-memoise + r-rtracklayer + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") (description "This package offers a statistical framework based on @@ -3894,39 +4105,39 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.32.1") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "0wq9y649dh1am6djzz0xlz42428xsgw2bdx1dknhdw2xbydmmx47")))) + "06kwf87h84xgswkrm7brmgr9aj1nf6cxp24hrfymkzq2pha5y5j7")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-category" ,r-category) - ("r-deseq2" ,r-deseq2) - ("r-edger" ,r-edger) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-gostats" ,r-gostats) - ("r-gseabase" ,r-gseabase) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-knitr" ,r-knitr) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-pfam-db" ,r-pfam-db) - ("r-r-utils" ,r-r-utils) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-category + r-deseq2 + r-edger + r-ggbio + r-ggplot2 + r-gostats + r-gseabase + r-hwriter + r-iranges + r-knitr + r-lattice + r-limma + r-pfam-db + r-r-utils + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/ReportingTools/") (synopsis "Tools for making reports in various formats") (description @@ -3944,19 +4155,18 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "1a5kw9ry9cr258al0x3q0ss5xn1ymscdypx51vzzgzamhy7dqakz")))) + "13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg")))) (build-system r-build-system) (propagated-inputs - `(("r-rhdf5filters" ,r-rhdf5filters) - ("r-rhdf5lib" ,r-rhdf5lib))) + (list r-rhdf5filters r-rhdf5lib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/rhdf5") (synopsis "HDF5 interface to R") (description @@ -3972,22 +4182,22 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "133v0s452acspi4dbf6gsa2xrr0qza86jdjjbpwhdv6zfd1djbgc")))) + "05b015pyp3g1crmm2d3ldsa7r5w0khmf87qbl4fv16r6pdggha78")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs - `(("r-rhdf5lib" ,r-rhdf5lib))) + (list r-rhdf5lib)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/grimbough/rhdf5filters") (synopsis "HDF5 compression filters") (description @@ -3998,13 +4208,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0arhh5bbx3pmxmkh5sjgczcswqy83d35r7cjhd2knpczdvrixaq5")))) + "0v6b3j45ivd9f04fpfs1vjwby5pi30mf5683bjxim01vi2krj9yh")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -4018,16 +4228,16 @@ HDF5 datasets.") (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") ""))))))) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bitops" ,r-bitops) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bitops + r-genomeinfodb + r-genomicranges + r-iranges + r-rhtslib + r-s4vectors + r-xvector)) (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") (synopsis "Interface to samtools, bcftools, and tabix") (description @@ -4053,11 +4263,7 @@ tab-delimited (tabix) files.") (properties `((upstream-name . "restfulr"))) (build-system r-build-system) (propagated-inputs - `(("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-yaml" ,r-yaml))) + (list r-rcurl r-rjson r-s4vectors r-xml r-yaml)) (home-page "https://cran.r-project.org/package=restfulr") (synopsis "R interface to RESTful web services") (description @@ -4067,13 +4273,13 @@ tab-delimited (tabix) files.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.52.1") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "11w6dx09pb49lin1gr9q88xn7ixh9jd5z6m9z27djchm0nw10lx9")))) + "11bh9khra2qdmicppi6ya43kf8f1z13ak92vkl6nr5f20k54cphc")))) (build-system r-build-system) (arguments `(#:phases @@ -4085,24 +4291,24 @@ tab-delimited (tabix) files.") (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") ""))))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocio" ,r-biocio) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-restfulr" ,r-restfulr) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) + (list zlib)) + (propagated-inputs + (list r-biocgenerics + r-biocio + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rcurl + r-restfulr + r-rsamtools + r-s4vectors + r-xml + r-xvector + r-zlibbioc)) (home-page "https://bioconductor.org/packages/rtracklayer") (synopsis "R interface to genome browsers and their annotation tracks") (description @@ -4128,13 +4334,13 @@ as well as query and modify the browser state, such as the current viewport.") (properties `((upstream-name . "samr"))) (build-system r-build-system) (propagated-inputs - `(("r-gsa" ,r-gsa) - ("r-impute" ,r-impute) - ("r-matrixstats" ,r-matrixstats) - ("r-openxlsx" ,r-openxlsx) - ("r-shiny" ,r-shiny) - ("r-shinyfiles" ,r-shinyfiles))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-gsa + r-impute + r-matrixstats + r-openxlsx + r-shiny + r-shinyfiles)) + (native-inputs (list gfortran)) (home-page "https://statweb.stanford.edu/~tibs/SAM/") (synopsis "Significance analysis of Microarrays") (description @@ -4143,21 +4349,61 @@ differential expression analysis, RNAseq data and related problems.") ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-scdblfinder + (package + (name "r-scdblfinder") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scDblFinder" version)) + (sha256 + (base32 "0wzmmcsnjybgzbc5rn4i72n26j9n59dfy1zg8ij0q8p4276jplsd")))) + (properties `((upstream-name . "scDblFinder"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-bluster + r-delayedarray + r-igraph + r-mass + r-matrix + r-s4vectors + r-scater + r-scran + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-xgboost)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/plger/scDblFinder") + (synopsis "Detect multiplets in single-cell RNA sequencing data") + (description + "The scDblFinder package gathers various methods for the detection and +handling of doublets/multiplets in single-cell RNA sequencing data (i.e. +multiple cells captured within the same droplet or reaction volume). It +includes methods formerly found in the scran package, and the new fast and +comprehensive scDblFinder method.") + (license license:gpl3))) + (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1253sj1hc6bbrff0iv5xa3v9znqvisll0fy6fdjka9c778fn4mcp")))) + "013hwj2lp29nqa8mkvm25aliarg0k725crg4cpsbj0iiskyrs6rl")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/seqLogo") (synopsis "Sequence logos for DNA sequence alignments") (description @@ -4169,22 +4415,18 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0h74z84zyvfzclsm0g13b95hirn99185wc6lp53jkzah9yyi59ay")))) + "1mik575qaxw9h9qyjn971207pfgbc8p1mx60jrb20jbrrihgg2na")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-plotrix" ,r-plotrix))) + (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix)) (home-page "https://bioconductor.org/packages/seqPattern") (synopsis "Visualising oligonucleotide patterns and motif occurrences") (description @@ -4196,35 +4438,35 @@ reference point and sorted by a user defined feature.") (define-public r-shortread (package (name "r-shortread") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0zqinw3c6h5v1c5nhzkiziirws16nbviccgw8nj2d22r33dbqwp3")))) + "1p17v15wd3v6w9ligpjjk28vy8k2ql57y2hhm8y6vnv9y3nagjsx")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-rhtslib" ,r-rhtslib) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) + (list zlib)) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-rhtslib + r-hwriter + r-iranges + r-lattice + r-latticeextra + r-rsamtools + r-s4vectors + r-xvector + r-zlibbioc)) (home-page "https://bioconductor.org/packages/ShortRead") (synopsis "FASTQ input and manipulation tools") (description @@ -4239,34 +4481,34 @@ ungapped alignment formats.") (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "0rqa414kvyjjmj4932zk39rqa14z13b57rkrxdrf16jmq2r437vh")))) + "05d9yjd8s7q1q78qmnx5xfrz9ppswc2cpfmjj47d338w783lwk98")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-circlize" ,r-circlize) - ("r-clue" ,r-clue) - ("r-cluster" ,r-cluster) - ("r-complexheatmap" ,r-complexheatmap) - ("r-digest" ,r-digest) - ("r-getoptlong" ,r-getoptlong) - ("r-go-db" ,r-go-db) - ("r-gosemsim" ,r-gosemsim) - ("r-matrix" ,r-matrix) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-proxyc" ,r-proxyc) - ("r-slam" ,r-slam) - ("r-tm" ,r-tm))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-circlize + r-clue + r-cluster + r-complexheatmap + r-digest + r-getoptlong + r-go-db + r-gosemsim + r-matrix + r-org-hs-eg-db + r-proxyc + r-slam + r-tm)) + (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/simplifyEnrichment") (synopsis "Simplify functional enrichment results") (description "This package provides a new clustering algorithm, binary @@ -4275,27 +4517,74 @@ this package. It also provides functionalities for visualizing, summarizing and comparing the clusterings.") (license license:expat))) +(define-public r-transcriptr + (package + (name "r-transcriptr") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "transcriptR" version)) + (sha256 + (base32 "1p5l2z3szx3qh02x7r81ajl7yc5wqsri6q6pzw83livmalcli5yy")))) + (properties `((upstream-name . "transcriptR"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-caret + r-chipseq + r-e1071 + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-proc + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/transcriptR") + (synopsis "Primary transcripts detection and quantification") + (description + "The differences in the RNA types being sequenced have an impact on the +resulting sequencing profiles. mRNA-seq data is enriched with reads derived +from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial +broader coverage of both exonic and intronic regions. The presence of +intronic reads in GRO-seq type of data makes it possible to use it to +computationally identify and quantify all de novo continuous regions of +transcription distributed across the genome. This type of data, however, is +more challenging to interpret and less common practice compared to mRNA-seq. +One of the challenges for primary transcript detection concerns the +simultaneous transcription of closely spaced genes, which needs to be properly +divided into individually transcribed units. The R package transcriptR +combines RNA-seq data with ChIP-seq data of histone modifications that mark +active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to +overcome this challenge. The advantage of this approach over the use of, for +example, gene annotations is that this approach is data driven and therefore +able to deal also with novel and case specific events.") + (license license:gpl3))) + (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "1b7mg3ypp1ay98cav47h9vn692lx0n9b5b0hpansgnkr5prb823b")))) + "0pzm1h69bg04a2v09r8c6pb3pix6f3n5dylvbv7wsp574qfaqyd1")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-igraph r-matrix r-s4vectors r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/TrajectoryUtils") (synopsis "Single-cell trajectory analysis utilities") (description @@ -4308,24 +4597,24 @@ structures to hold pseudotime inference results.") (define-public r-slingshot (package (name "r-slingshot") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "1aqsz2kxwax8d8d5iv3zk5hlyk5aya1wbxs1wky2rgccw4d35whx")))) + "081kp9b0lpw2xq9xvd2kykqqrqcj322mp7xa44xc3kf0nzsivqfa")))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrixstats" ,r-matrixstats) - ("r-princurve" ,r-princurve) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-trajectoryutils" ,r-trajectoryutils))) + (list r-igraph + r-matrixstats + r-princurve + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-trajectoryutils)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/slingshot") (synopsis "Tools for ordering single-cell sequencing") (description "This package provides functions for inferring continuous, @@ -4337,34 +4626,67 @@ events and allows for the incorporation of prior knowledge through supervised graph construction.") (license license:artistic2.0))) +(define-public r-stringdb + (package + (name "r-stringdb") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "STRINGdb" version)) + (sha256 + (base32 "1hvb73anhbf1g82nn5m11s783z6ihvlavf7p30w29qggxggnl6lm")))) + (properties `((upstream-name . "STRINGdb"))) + (build-system r-build-system) + (propagated-inputs + (list r-gplots + r-hash + r-igraph + r-plotrix + r-plyr + r-png + r-rcolorbrewer + r-rcurl + r-sqldf)) + (home-page "https://git.bioconductor.org/packages/STRINGdb") + (synopsis "Search tool for the retrieval of interacting proteins database") + (description + "The @code{STRINGdb} package provides an R interface to the STRING +protein-protein interactions database. @url{https://www.string-db.org, +STRING} is a database of known and predicted protein-protein interactions. +The interactions include direct (physical) and indirect (functional) +associations. Each interaction is associated with a combined confidence score +that integrates the various evidences.") + (license license:gpl2))) + (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.8.2") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "04ac4mjh3pgdlws0aiacqg0vd7bhg890w44r7b90p947c3rk1mfw")))) - (build-system r-build-system) - (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rlang" ,r-rlang) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (base32 "009l27kb9gvwwf57dwxfribhfhvn4z5pw8yc847l6pkbzqggx678")))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-biocgenerics + r-biostrings + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-rlang + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/") (synopsis "R package designed to simplify structural variant analysis") (description @@ -4377,28 +4699,28 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "16np5ik6jgbi68mhlib6yskywwbaa50mlr7m3sh1hqk889whfn1g")))) + "0qpnx2aii9vs7fcp0ax5j77ysbhi4qhjhm35vnygs3isbrjn925a")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase + r-biocgenerics + r-delayedarray + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-matrixgenerics + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/SummarizedExperiment") (synopsis "Container for representing genomic ranges by sample") (description @@ -4411,22 +4733,22 @@ samples.") (define-public r-sva (package (name "r-sva") - (version "3.40.0") + (version "3.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "12jkcybdfspabh7x124d44l9fj1hwwg3gvcqxvz5wpkiflc2vkji")))) + "0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj")))) (build-system r-build-system) (propagated-inputs - `(("r-edger" ,r-edger) - ("r-genefilter" ,r-genefilter) - ("r-mgcv" ,r-mgcv) - ("r-biocparallel" ,r-biocparallel) - ("r-matrixstats" ,r-matrixstats) - ("r-limma" ,r-limma))) + (list r-edger + r-genefilter + r-mgcv + r-biocparallel + r-matrixstats + r-limma)) (home-page "https://bioconductor.org/packages/sva") (synopsis "Surrogate variable analysis") (description @@ -4442,46 +4764,32 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.26.3") + (version "2.0.5") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "01l35l5zj87qkarrbal9la6kshk3j7k8hy3iimv3gdnnz4axmvs7")))) + "1j91pyfjsqngxxlxjqc477pznlfax4vayrks2q12rxw76ija80hf")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-assertthat" ,r-assertthat) - ("r-batchtools" ,r-batchtools) - ("r-biostrings" ,r-biostrings) - ("r-crayon" ,r-crayon) - ("r-deseq2" ,r-deseq2) - ("r-dot" ,r-dot) - ("r-edger" ,r-edger) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-go-db" ,r-go-db) - ("r-gostats" ,r-gostats) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-pheatmap" ,r-pheatmap) - ("r-rjson" ,r-rjson) - ("r-rsamtools" ,r-rsamtools) - ("r-rsvg" ,r-rsvg) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-testthat" ,r-testthat) - ("r-yaml" ,r-yaml) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-crayon + r-genomicranges + r-ggplot2 + r-htmlwidgets + r-magrittr + r-rsamtools + r-s4vectors + r-shortread + r-stringr + r-summarizedexperiment + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/tgirke/systemPipeR") (synopsis "Next generation sequencing workflow and reporting environment") (description @@ -4499,26 +4807,26 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1ggi7yrhkyi85p3sfj3yd95n9mzq1xpff28ixa4dl9yzasks1v5a")))) + "01vykf8bzwm2k7cfj09r6il6qaycjy10wpaxbn13f21p66r5nlm2")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dbi" ,r-dbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-lattice" ,r-lattice) - ("r-matrixstats" ,r-matrixstats) - ("r-sparsem" ,r-sparsem))) + (list r-annotationdbi + r-dbi + r-biobase + r-biocgenerics + r-go-db + r-graph + r-lattice + r-matrixstats + r-sparsem)) (home-page "https://bioconductor.org/packages/topGO") (synopsis "Enrichment analysis for gene ontology") (description @@ -4532,16 +4840,16 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0ip2yr0zspf2aagskxl4dwncr48dw5qb90an3sswnnh2dqdb82if")))) + "0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") (description @@ -4553,37 +4861,70 @@ provided as a matrix which can be used as an offset for different expression of gene-level counts.") (license license:gpl2+))) +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-valr + (package + (name "r-valr") + (version "0.6.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "valr" version)) + (sha256 + (base32 + "0dd41irvibh6rwi52bw4zg4m7wpyihlp1kdkb8fdji3csw2fiz4k")))) + (build-system r-build-system) + (propagated-inputs + (list r-broom + r-dplyr + r-ggplot2 + r-rcpp + r-readr + r-rlang + r-rtracklayer ;bioconductor package + r-stringr + r-tibble)) + (native-inputs + (list r-knitr)) + (home-page "https://github.com/rnabioco/valr") + (synopsis "Genome interval arithmetic in R") + (description + "This package enables you to read and manipulate genome intervals and +signals. It provides functionality similar to command-line tool suites within +R, enabling interactive analysis and visualization of genome-scale data.") + (license license:expat))) + (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "0c9r00j8a3bs6n0dv4wi17jc1ljzvr3r2bi4h9axhcsf2ip906rh")))) + "1r9kayp0hxcwls08lv2fh0cmf9ks0lqx3k31c1zn4asw4dyqpgva")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biostrings + r-bsgenome + r-dbi + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-matrixgenerics + r-summarizedexperiment + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector + r-zlibbioc)) (build-system r-build-system) (home-page "https://bioconductor.org/packages/VariantAnnotation") (synopsis "Package for annotation of genetic variants") @@ -4594,23 +4935,19 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.60.0") + (version "3.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "0nppph3kv8z83368snb8s3n4vcqj829yyi1kh4q09qvq18rhvssv")))) + "03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-ggplot2" ,r-ggplot2) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma))) + (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") (synopsis "Variance stabilization and calibration for microarray data") (description @@ -4627,16 +4964,79 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) +(define-public r-xina + (package + (name "r-xina") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "XINA" version)) + (sha256 + (base32 "14j1rn3p7i0rlqkbbg0a6pyhb97ifzvsbw6vfxw9pna7zv7rbhsp")))) + (properties `((upstream-name . "XINA"))) + (build-system r-build-system) + (propagated-inputs + (list r-alluvial + r-ggplot2 + r-gridextra + r-igraph + r-mclust + r-plyr + r-stringdb)) + (native-inputs (list r-knitr)) + (home-page "https://git.bioconductor.org/packages/XINA") + (synopsis "Identifying proteins that exhibit similar patterns") + (description + "The aim of @code{XINA} is to determine which proteins exhibit similar +patterns within and across experimental conditions, since proteins with +co-abundance patterns may have common molecular functions. @code{XINA} imports +multiple datasets, tags dataset in silico, and combines the data for subsequent +subgrouping into multiple clusters. The result is a single output depicting +the variation across all conditions. @code{XINA} not only extracts +coabundance profiles within and across experiments, but also incorporates +protein-protein interaction databases and integrative resources such as +@dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and +molecular functions, respectively, and produces intuitive graphical outputs.") + (license license:gpl3))) + +(define-public r-xmapbridge + (package + (name "r-xmapbridge") + (version "1.52.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "xmapbridge" version)) + (sha256 + (base32 "1zsqhisbq6f9qgw9f0a6ixxh635h3qm17117yfns5nnfw73ndlgi")))) + (properties `((upstream-name . "xmapbridge"))) + (build-system r-build-system) + (home-page "https://git.bioconductor.org/packages/xmapbridge") + (synopsis "Display numeric data in the web based genome browser X:MAP") + (description + "The package @code{xmapbridge} can plot graphs in the X:Map genome +browser. X:Map uses the Google Maps API to provide a scrollable view of the +genome. It supports a number of species, and can be accessed at +@url{http://xmap.picr.man.ac.uk}. This package exports plotting files in a +suitable format. Graph plotting in R is done using calls to the functions +@code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be +similar to those used by the standard plot methods in R. These result in data +being written to a set of files (in a specific directory structure) that +contain the data to be displayed, as well as some additional meta-data +describing each of the graphs.") + (license license:lgpl3))) + (define-public r-xvector (package (name "r-xvector") - (version "0.32.0") + (version "0.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1cw34gd9iaspl0v737xl7rngq63zrj03a5ngai15ggrnv1sq2aqr")))) + "07r4qgmnifw9jk2srjg0cvl310j0f9y35jrg0zqhlvhmyhg6n2c0")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -4651,11 +5051,9 @@ and specific in detecting differential transcription.") (("import\\(zlibbioc\\)") "")) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-iranges r-s4vectors)) (home-page "https://bioconductor.org/packages/XVector") (synopsis "Representation and manpulation of external sequences") (description @@ -4666,13 +5064,13 @@ and specific in detecting differential transcription.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "1dv5bf12kzk1yzyfs3g5syim16sbi44kalvzj2i2xcnxnl6x60ip")))) + "0a0dl7z58zxdj6938zbxixphgljj1giylk1nd05bb7qsccmp0xhj")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -4682,25 +5080,57 @@ and specific in detecting differential transcription.") libraries for systems that do not have these available via other means.") (license license:artistic2.0))) +(define-public r-zellkonverter + (package + (name "r-zellkonverter") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "zellkonverter" version)) + (sha256 + (base32 "1ihp2f23lpdfgf3qliy22vrq8czm353hyhqf74r5r712190k6pgg")))) + (properties `((upstream-name . "zellkonverter"))) + (build-system r-build-system) + (propagated-inputs + (list r-basilisk + r-cli + r-delayedarray + r-matrix + r-reticulate + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/theislab/zellkonverter") + (synopsis "Conversion between AnnData and single-cell experiments objects") + (description + "This package provides methods to convert between Python AnnData objects +and SingleCellExperiment objects. These are primarily intended for use by +downstream Bioconductor packages that wrap Python methods for single-cell data +analysis. It also includes functions to read and write H5AD files used for +saving AnnData objects to disk.") + (license license:expat))) + (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "1d085lfa3yif5wkys1fb0zzgg0cqwd1y18vasgqqdr6rva075d4z")))) + "1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8")))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-lattice" ,r-lattice) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-lattice + r-rcolorbrewer)) (home-page "https://bioconductor.org/packages/geneplotter") (synopsis "Graphics functions for genomic data") (description @@ -4710,30 +5140,30 @@ libraries for systems that do not have these available via other means.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "1nsfyfpj264h6y322pzz0i001b0m862j3skbq5rjwlrj1p8j2gi7")))) + "1ia2f19swiwb0552nfwkai4gl0av07cj75b6jwiviqa1bli09264")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs - `(("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-ff" ,r-ff) - ("r-foreach" ,r-foreach) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-affyio + r-biobase + r-biocgenerics + r-biocmanager + r-biostrings + r-dbi + r-ff + r-foreach + r-genomicranges + r-iranges + r-rsqlite + r-s4vectors + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/oligoClasses/") (synopsis "Classes for high-throughput arrays") (description @@ -4745,31 +5175,31 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0fyq77im6s79havjwbchhqhnllxs134jsi98g6msxz66h16lj3al")))) + "1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-affxparser" ,r-affxparser) - ("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-ff" ,r-ff) - ("r-oligoclasses" ,r-oligoclasses) - ("r-preprocesscore" ,r-preprocesscore) - ("r-rsqlite" ,r-rsqlite) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (inputs (list zlib)) + (propagated-inputs + (list r-affxparser + r-affyio + r-biobase + r-biocgenerics + r-biostrings + r-dbi + r-ff + r-oligoclasses + r-preprocesscore + r-rsqlite + r-zlibbioc)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/oligo/") (synopsis "Preprocessing tools for oligonucleotide arrays") (description @@ -4781,20 +5211,19 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "0xssanffh1hr7f48mnazcpwi25rdp7mxlyb9nbf4q2mp7m40jnpm")))) + "1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2))) + (list r-ggplot2 r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/StoreyLab/qvalue") (synopsis "Q-value estimation for false discovery rate control") (description @@ -4836,23 +5265,23 @@ integration with @code{Rcpp}.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "1xld6ar440achik4dbd7vhiw6jfj0sb96jm52n7hav5bv4gag3mh")))) + "11w4vyc1sllmm5lh42krhidazid78n4s3lhikpy9kk2l57jmifbr")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs - `(("r-emdbook" ,r-emdbook) - ("r-genomicranges" ,r-genomicranges) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppnumerical" ,r-rcppnumerical) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-emdbook + r-genomicranges + r-rcpp + r-rcppeigen + r-rcppnumerical + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/apeglm") (synopsis "Approximate posterior estimation for GLM coefficients") (description "This package provides Bayesian shrinkage estimators for @@ -4863,24 +5292,24 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "1g9ja8p90czx83ar0l9ran7m6aggvszdbqm714fq7z4rxq9b4hs3")))) + "1h7h27q6l9d8j0shklyrh135zrwx56v4zzmm21cj1b7dvmwvpbcv")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-mass" ,r-mass) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-mass + r-rsamtools + r-rtracklayer + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/GreyListChIP") (synopsis "Greylist artefact regions based on ChIP inputs") (description "This package identifies regions of ChIP experiments with high @@ -4890,40 +5319,40 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.2.7") + (version "3.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "01jfxcj5c0088vvsi3pz8fs0ka6n12l2j8s1d0rpqwa1y0444x7z")))) + "1bz03ls7pkb09p6nkz7gfnhjlh06mgbp3j98ppnzibiar3cjrnfj")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs - `(("r-amap" ,r-amap) - ("r-apeglm" ,r-apeglm) - ("r-ashr" ,r-ashr) - ("r-biocparallel" ,r-biocparallel) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gplots" ,r-gplots) - ("r-greylistchip" ,r-greylistchip) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-rcolorbrewer" , r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-systempiper" ,r-systempiper))) + (list r-amap + r-apeglm + r-ashr + r-biocparallel + r-deseq2 + r-dplyr + r-genomicalignments + r-genomicranges + r-ggplot2 + r-ggrepel + r-gplots + r-greylistchip + r-iranges + r-lattice + r-limma + r-locfit + r-rcolorbrewer + r-rcpp + r-rhtslib + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-systempiper)) (home-page "https://bioconductor.org/packages/DiffBind") (synopsis "Differential binding analysis of ChIP-Seq peak data") (description @@ -4946,13 +5375,13 @@ occupancy (overlap) analysis and plotting functions.") (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-rsamtools" ,r-rsamtools) - ("r-genomicalignments" ,r-genomicalignments) - ("r-rtracklayer" ,r-rtracklayer))) + (list r-s4vectors + r-iranges + r-genomicranges + r-summarizedexperiment + r-rsamtools + r-genomicalignments + r-rtracklayer)) (home-page "https://bioconductor.org/packages/RIPSeeker") (synopsis "Identifying protein-associated transcripts from RIP-seq experiments") @@ -4968,29 +5397,29 @@ processing to visualization and annotation.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "1k7ngpx4s50jplrsv19zzjr7izpdl9wwppb218ih5cp0ki1gcc2n")))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-benchmarkme" ,r-benchmarkme) - ("r-biocparallel" ,r-biocparallel) - ("r-clusterr" ,r-clusterr) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + "03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k")))) + (build-system r-build-system) + (native-inputs + (list r-knitr)) + (propagated-inputs + (list r-beachmat + r-benchmarkme + r-biocparallel + r-clusterr + r-delayedarray + r-matrix + r-rcpp + r-rcpparmadillo + r-rhdf5lib + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/mbkmeans") (synopsis "Mini-batch k-means clustering for single-cell RNA-seq") (description "This package implements the mini-batch k-means algorithm for @@ -5000,20 +5429,17 @@ large datasets, including support for on-disk data representation.") (define-public r-multtest (package (name "r-multtest") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "1wi15v4llgv11hpb2j9h4a35nrnawnmvbz5d5dvgy8lhqrlq8w9a")))) + "03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns")))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biobase" ,r-biobase) - ("r-mass" ,r-mass))) + (list r-survival r-biocgenerics r-biobase r-mass)) (home-page "https://bioconductor.org/packages/multtest") (synopsis "Resampling-based multiple hypothesis testing") (description @@ -5038,16 +5464,16 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1i7s198d5kw4gk6nqqsd3vqaknj4493p822f2za8q95gv6x02rxa")))) + "0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) + (list r-biocgenerics)) (home-page "https://bioconductor.org/packages/graph") (synopsis "Handle graph data structures in R") (description @@ -5069,8 +5495,7 @@ expressed genes in DNA microarray experiments.") (properties `((upstream-name . "ggm"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-igraph" ,r-igraph))) + (list r-graph r-igraph)) (home-page "https://cran.r-project.org/package=ggm") (synopsis "Functions for graphical Markov models") (description @@ -5093,9 +5518,7 @@ fitting of some classes of graphical Markov models.") (properties `((upstream-name . "PerfMeas"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-limma" ,r-limma) - ("r-rbgl" ,r-rbgl))) + (list r-graph r-limma r-rbgl)) (home-page "https://cran.r-project.org/web/packages/PerfMeas/") (synopsis "Performance measures for ranking and classification tasks") (description @@ -5119,9 +5542,7 @@ a given recall, F-score for single and multiple classes are available.") (properties `((upstream-name . "CodeDepends"))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-graph" ,r-graph) - ("r-xml" ,r-xml))) + (list r-codetools r-graph r-xml)) (home-page "https://cran.r-project.org/web/packages/CodeDepends") (synopsis "Analysis of R code for reproducible research and code comprehension") (description @@ -5136,44 +5557,44 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.26.4") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1iqzm7pifl9zrw3s06i6h85n1p01pd06vh1a93izyfhgybxn262d")))) + "05fbq8zvww1nlyykrri0hf4248i1i7w5cr453giagmjq7lgg4v3b")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-dplyr" ,r-dplyr) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-graph" ,r-graph) - ("r-interactionset" ,r-interactionset) - ("r-iranges" ,r-iranges) - ("r-keggrest" ,r-keggrest) - ("r-matrixstats" ,r-matrixstats) - ("r-multtest" ,r-multtest) - ("r-rbgl" ,r-rbgl) - ("r-regioner" ,r-regioner) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-venndiagram" ,r-venndiagram))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-biomart + r-biostrings + r-dbi + r-dplyr + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-graph + r-interactionset + r-iranges + r-keggrest + r-matrixstats + r-multtest + r-rbgl + r-regioner + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-venndiagram)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/ChIPpeakAnno") (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") (description @@ -5190,18 +5611,18 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.4.3") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1yir3rwhz5vf0pdn3fpvlc57c75k98gvv8gapajbvymz3lyghijv")))) + "1s75p8rrmj24r0vcbaiyw8xg8y84j388mv6iawai7pypfcl8s1z3")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) (propagated-inputs - `(("r-matrixstats" ,r-matrixstats))) + (list r-matrixstats)) (home-page "https://bioconductor.org/packages/MatrixGenerics") (synopsis "S4 generic summary statistic functions for matrix-like objects") (description @@ -5217,15 +5638,15 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "0wpmrhqpyv27h1hn31hzz21r74r7yqx79ljv8i8gn6ix8lf5ca56")))) + (base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz")))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma))) + (list r-limma)) (home-page "https://bioconductor.org/packages/marray") (synopsis "Exploratory analysis for two-color spotted microarray data") (description "This package contains class definitions for two-color spotted @@ -5236,17 +5657,16 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1p87k4vw981k97d9bckmprrfg55jwd91658rgxzjj8hnschf28a4")))) + (base32 "1kfxw126bddfy67cmf8dca9qq4bg7fkxjf8iaikplhvs5hl7bp4d")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-marray" ,r-marray))) + (list r-biobase r-marray)) (home-page "https://bioconductor.org/packages/CGHbase") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by @@ -5256,20 +5676,16 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1zik04y2q0anzy85l0b4ryzkxpfx2fnmpwp5s7akyk1jfl2r8gw7")))) + (base32 "1r4y8zakgmdbnpwgp14kwh4iwqgqcmjq2yg4nc7j37p09bw1c8zr")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-cghbase" ,r-cghbase) - ("r-impute" ,r-impute) - ("r-dnacopy" ,r-dnacopy) - ("r-snowfall" ,r-snowfall))) + (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall)) (home-page "https://bioconductor.org/packages/CGHcall") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by @@ -5279,26 +5695,25 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1p4544xlarkbgs9kybrrawq3v7qr6ix62nrc6l7dcksh2ka69yzf")))) + (base32 "1sza9br8agpdz1k9fn5wisir44sj8v0rk4wbx35d2c2kp9q70pqj")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-cghbase" ,r-cghbase) - ("r-cghcall" ,r-cghcall) - ("r-dnacopy" ,r-dnacopy) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-r-utils" ,r-r-utils) - ("r-rsamtools" ,r-rsamtools))) + (list r-biobase + r-cghbase + r-cghcall + r-dnacopy + r-future-apply + r-genomicranges + r-iranges + r-matrixstats + r-r-utils + r-rsamtools)) (home-page "https://bioconductor.org/packages/QDNAseq") (synopsis "Quantitative DNA sequencing for chromosomal aberrations") (description "The genome is divided into non-overlapping fixed-sized bins, @@ -5312,20 +5727,18 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "0hyc0sl2nf18bz0jxbzim0v41zwh2rnnr7l3p6zkk9wnw5gn7bbc")))) + "1zgxwb287ccz4wqsjxmffknnzziv12l4yrw7df912dxz6yccvd8r")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-edger" ,r-edger) - ("r-genomicranges" ,r-genomicranges))) + (list r-abind r-edger r-genomicranges)) (home-page "https://bioconductor.org/packages/baySeq/") (synopsis "Bayesian analysis of differential expression patterns in count data") (description @@ -5338,27 +5751,27 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "1kfxjh1mynrgqsy2q6byf03cbymqc8w7l7672iyd0wj5qzlif4h5")))) + "1wdy92y5l3wa3zgg59w69rd7gdwf4z1waa4i2cccniccz463p1xq")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics + r-bsgenome-hsapiens-ucsc-hg19 + r-bsgenome-mmusculus-ucsc-mm9 + r-genomeinfodb + r-genomicranges + r-iranges + r-limma + r-rsamtools + r-rtracklayer + r-s4vectors)) (home-page "https://bioconductor.org/packages/ChIPComp") (synopsis "Quantitative comparison of multiple ChIP-seq datasets") (description @@ -5372,35 +5785,35 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "1jmd8yrv7p7hn4gdibg3svmhqxjyrnfp7cgsqg8zv862lgd75zsl")))) + "1szlzvm8ggjc40k4z2fxxa2h28g6j9wj2g5aw480v9hgyvvdw5lx")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-sqldf" ,r-sqldf))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-data-table + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggbio + r-ggplot2 + r-iranges + r-plyr + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-sqldf)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/RiboProfiling/") (synopsis "Ribosome profiling data analysis") (description "Starting with a BAM file, this package provides the @@ -5413,24 +5826,24 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1m5w2j35wr0lzwir4s58z757vrcsj5mglsqrkvs241k0hlmn06qa")))) + "0nnhjvjl4c9yyfzjf8kcj4yky5cdimicp7lz008sczy19jq4vjhd")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-bayseq" ,r-bayseq) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-seqlogo" ,r-seqlogo))) + (list r-abind + r-bayseq + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-seqlogo)) (home-page "https://bioconductor.org/packages/riboSeqR/") (synopsis "Analysis of sequencing data from ribosome profiling experiments") (description @@ -5441,28 +5854,28 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "034xidjmn67n1471fnpdmz7gjm6p05cj8sp9nssc3gxdzn54a6xb")))) + "19m2mpby73zanai68rlqvzx9zccli4dz4kix93acrw9755xp3bsw")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-rcpp + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/InteractionSet") (synopsis "Base classes for storing genomic interaction data") (description @@ -5475,36 +5888,36 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0zjl7rp5fk14kqsx0bkbpq6hqahbkiyvwa9aggp4kfb8hnmz9qal")))) + "090kxq5jn1jfr9fgbkvbjr5g4bcxzgsaal3gc9yx1n7pgmhccfmb")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gviz" ,r-gviz) - ("r-igraph" ,r-igraph) - ("r-interactionset" ,r-interactionset) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-data-table + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-gviz + r-igraph + r-interactionset + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-stringr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") (synopsis "R package for handling genomic interaction data") (description @@ -5516,16 +5929,16 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "1v8aysvy6a3r1iafc3xvk885c128kb3pb9zpcdhdjcn0by96k8hh")))) + "1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx")))) (build-system r-build-system) - (propagated-inputs `(("r-amap" ,r-amap))) + (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") (synopsis "Cluster and tree conversion") (description @@ -5536,22 +5949,22 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "07qrxssx4rb8r958r1smx8xfpzdxpp55hci3201hcmz3mxz77i0s")))) + "1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biasedurn" ,r-biasedurn) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genelendatabase" ,r-genelendatabase) - ("r-go-db" ,r-go-db) - ("r-mgcv" ,r-mgcv))) + (list r-annotationdbi + r-biasedurn + r-biocgenerics + r-genelendatabase + r-go-db + r-mgcv)) (home-page "https://bioconductor.org/packages/goseq/") (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") (description @@ -5562,26 +5975,26 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0dsk8qmwimzmd1x4k4jwg9q11jm1ahn8cw0gzd6s2gmigfls4hsa")))) + "0qkbx9n2vb7kvb5f00csnbffy5bm7hhbdvkx2isgzi0wv0y59kx9")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs - `(("r-deseq2" ,r-deseq2) - ("r-edger" ,r-edger) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-limma" ,r-limma) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-deseq2 + r-edger + r-htmlwidgets + r-jsonlite + r-limma + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Shians/Glimma") (synopsis "Interactive HTML graphics") (description @@ -5595,19 +6008,18 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "18wyi73l95df182vg3m014sxwdbpggr61vsbazhyw4vyx2fnzmpl")))) + "0qhy984y83a3nf4zw54rasw3vn932q4zb3gljifkw701jnrzqmki")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-rcpp" ,r-rcpp))) + (list r-biobase r-rcpp)) (home-page "https://bioconductor.org/packages/ROTS/") (synopsis "Reproducibility-Optimized Test Statistic") (description @@ -5619,18 +6031,17 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "1rz5jk5bgpk7gjknx79jyslahjg46q2f4bx6dgd0vwmarc29a45z")))) + "06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-mass" ,r-mass))) + (list r-biobase r-mass)) (home-page "http://www.genopolis.it") (synopsis "Detect differential expression in microarray and proteomics datasets") (description @@ -5644,41 +6055,40 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0jh5db9dv5pb6b50sg22x8q55m3h0h0nkmb9mivvvp22dhyrd82z")))) + "072kv5k3giyll1clzrg0anqhyl4qbi7cjnmkqz25zdl5bab9l7jk")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-deseq2" ,r-deseq2) - ("r-desolve" ,r-desolve) - ("r-gdata" ,r-gdata) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-plgem" ,r-plgem) - ("r-proc" ,r-proc) - ("r-rootsolve" ,r-rootsolve) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-txdb-mmusculus-ucsc-mm9-knowngene" - ,r-txdb-mmusculus-ucsc-mm9-knowngene))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-deseq2 + r-desolve + r-gdata + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-kernsmooth + r-plgem + r-proc + r-rootsolve + r-rsamtools + r-rtracklayer + r-s4vectors + r-shiny + r-summarizedexperiment + r-txdb-mmusculus-ucsc-mm9-knowngene)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/INSPEcT") (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") (description @@ -5691,22 +6101,20 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "1wiqmzjcb7flp7ldcgbx91asxxrmm1rg9pcfljniab9xcsldhksp")))) + "07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-bh r-matrix r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/DNABarcodes") (synopsis "Create and analyze DNA barcodes") (description @@ -5720,23 +6128,20 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "1fy0k1p0m209lzjpd5jhfnifa22lrn63qq3a3kn5g0xhbbmijzac")))) + "1a19klscykdgsd7izcxyr45ml7g0gpdj65gvbaw124mal2p4zi9q")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-edaseq" ,r-edaseq) - ("r-edger" ,r-edger) - ("r-mass" ,r-mass))) + (list r-biobase r-edaseq r-edger r-mass)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/drisso/RUVSeq") (synopsis "Remove unwanted variation from RNA-Seq data") (description @@ -5748,24 +6153,20 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "0cjidi18wjip9xzx83890wjk40vvjq06prf1ag4m2kac47w01r7v")))) + "04in8l6j7frgm0a5dzphazfhn9cm8w775z5yir712jxa37mh1agr")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpphnsw" ,r-rcpphnsw) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocNeighbors") (synopsis "Nearest Neighbor Detection for Bioconductor packages") (description @@ -5780,21 +6181,19 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "1j96fvw1waqxbv5c8myfmhsidq370z03yz13yqmrs4nn1rpn1a06")))) + "0vz8441gl5gycy1ypybwhq97bnyvhhlg6gxpi1dsdy2c9b6d81kc")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-delayedarray r-matrix r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://github.com/LTLA/ScaledMatrix") (synopsis "Create a DelayedMatrix of scaled and centered values") (description @@ -5808,25 +6207,25 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.16.2") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "1y60yvg1rl21cab9xrkns0209pg44mwr90qj099dvk97wsjkx67g")))) + "19i8jhvycv57zbxhpn5gx5ymdiws64kc3nidc00xh1j9a8xkj1aq")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-dplyr" ,r-dplyr) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidytree" ,r-tidytree))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ape + r-dplyr + r-jsonlite + r-magrittr + r-rlang + r-tibble + r-tidytree)) + (native-inputs (list r-knitr)) (home-page "https://github.com/YuLab-SMU/treeio") (synopsis "Base classes and functions for Phylogenetic tree input and output") (description @@ -5840,31 +6239,31 @@ platform for merging tree with associated data and converting file formats.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.0.4") + (version "3.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "0xf4b9vfdyzzivwgw4ymapl5bb4k9p04mmr53822kxgfd5qrs1zx")))) + "0qk39gdpy4kznjhmvi25y2spcdj2r1i6mv673vx8dzf66zfs20v8")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-aplot" ,r-aplot) - ("r-dplyr" ,r-dplyr) - ("r-ggfun" ,r-ggfun) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tidyr" ,r-tidyr) - ("r-tidytree" ,r-tidytree) - ("r-treeio" ,r-treeio) - ("r-yulab-utils" ,r-yulab-utils))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ape + r-aplot + r-dplyr + r-ggfun + r-ggplot2 + r-magrittr + r-purrr + r-rlang + r-scales + r-tidyr + r-tidytree + r-treeio + r-yulab-utils)) + (native-inputs (list r-knitr)) (home-page "https://yulab-smu.top/treedata-book/") (synopsis "R package for visualization of trees and annotation data") (description @@ -5877,20 +6276,20 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "1hbcwr6d8gyrf4azh0gi588xkrg6gz7gsb5hbvzqkhplbsp6shlv")))) + "1s8dfzpgbpxbn3jvx891gvw3jyn43nlxb73yv1vjn85brk9zbqpk")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/metapod") (synopsis "Meta-analyses on p-values of differential analyses") (description @@ -5906,29 +6305,29 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "16gkwq8fb8jdchpnlzq2hz3i74a6pzbnc1bf93282h11mp7qr58l")))) + "0dkh6a23qymjcynppmpp3k1mzpfadv8dqyz410pxkqsxig4ldd4n")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-delayedarray" ,r-delayedarray) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rsvd" ,r-rsvd) - ("r-s4vectors" ,r-s4vectors) - ("r-scaledmatrix" ,r-scaledmatrix))) + (list r-beachmat + r-biocgenerics + r-biocparallel + r-delayedarray + r-irlba + r-matrix + r-rcpp + r-rsvd + r-s4vectors + r-scaledmatrix)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/LTLA/BiocSingular") (synopsis "Singular value decomposition for Bioconductor packages") (description @@ -5941,40 +6340,40 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.4.0") + (version "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-ggplot-multistats" ,r-ggplot-multistats) - ("r-ggplot2" ,r-ggplot2) - ("r-ggthemes" ,r-ggthemes) - ("r-irlba" ,r-irlba) - ("r-knn-covertree" ,r-knn-covertree) - ("r-matrix" ,r-matrix) - ("r-pcamethods" ,r-pcamethods) - ("r-proxy" ,r-proxy) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcpphnsw" ,r-rcpphnsw) - ("r-rspectra" ,r-rspectra) - ("r-scales" ,r-scales) - ("r-scatterplot3d" ,r-scatterplot3d) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-smoother" ,r-smoother) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-vim" ,r-vim))) - (native-inputs - `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes + "01662p5j9l12ylf5a5djg4cjppd2n3chrygzw8nnrcf1806xn58y")))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-ggplot-multistats + r-ggplot2 + r-ggthemes + r-irlba + r-knn-covertree + r-matrix + r-pcamethods + r-proxy + r-rcpp + r-rcppeigen + r-rcpphnsw + r-rspectra + r-scales + r-scatterplot3d + r-singlecellexperiment + r-smoother + r-summarizedexperiment + r-tidyr + r-tidyselect + r-vim)) + (native-inputs + (list r-nbconvertr)) ; for vignettes (home-page "https://bioconductor.org/packages/destiny/") (synopsis "Create and plot diffusion maps") (description "This package provides tools to create and plot diffusion @@ -5985,22 +6384,18 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "1ynp334hm76zf05j4f6vha6r16s5f2ncxx9yviq4rxidk9r723jq")))) + "0dwl94j5dm5ngn8lyyc4bd9ihd1nqincvq26najjn6lw0x55ciky")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales) - ("r-xml" ,r-xml))) + (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml)) (home-page "https://github.com/bcalder/savR") (synopsis "Parse and analyze Illumina SAV files") (description @@ -6011,36 +6406,36 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "0fbrf5s6pz115djm7xw95k1d0p7svi40aacbb3d52wmx5azwj424")))) + "1hh3mhfcngyx7cpzns8mjqviy8vfzrvxpv6nyizflpfmsr39mxfk")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-biovizbase" ,r-biovizbase) - ("r-broom" ,r-broom) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hexbin" ,r-hexbin) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-biovizbase + r-broom + r-data-table + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-hexbin + r-iranges + r-rcolorbrewer + r-rmarkdown + r-rsamtools + r-s4vectors + r-scales + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/keleslab/ChIPexoQual") (synopsis "Quality control pipeline for ChIP-exo/nexus data") (description @@ -6051,19 +6446,16 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "03pvjzjrcsbjfw3855s3whfzin45vaipy7cahnj6fywdysvh8hps")))) + "143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534")))) (build-system r-build-system) (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-biocgenerics" ,r-biocgenerics))) + (list r-s4vectors r-iranges r-genomicranges r-biocgenerics)) (home-page "https://bioconductor.org/packages/copynumber") (synopsis "Segmentation of single- and multi-track copy number data") (description @@ -6074,17 +6466,17 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0mgq814f6c2271d2lxg763bsnv3ma4ari5xa4x1rbksv8yvcjc4d")))) + "19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://bioconductor.org/packages/DNAcopy") (synopsis "DNA copy number data analysis") (description @@ -6109,9 +6501,7 @@ abnormal copy number.") (properties `((upstream-name . "HTSCluster"))) (build-system r-build-system) (propagated-inputs - `(("r-capushe" ,r-capushe) - ("r-edger" ,r-edger) - ("r-plotrix" ,r-plotrix))) + (list r-capushe r-edger r-plotrix)) (home-page "https://cran.r-project.org/web/packages/HTSCluster") (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") (description @@ -6163,7 +6553,7 @@ and summarizing a set of statistics using a weighted distance approach.") (properties `((upstream-name . "NBPSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-qvalue" ,r-qvalue))) + (list r-qvalue)) (home-page "https://cran.r-project.org/web/packages/NBPSeq") (synopsis "Negative binomial models for RNA-Seq data") (description @@ -6174,20 +6564,18 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "0h5v3vrb90zim80bdnr3aw58g3h7zjqa4l9i0jwx5j19ywf54fdz")))) + "1p8i04v5h6mbc8zqbf3rifbwwylzzc1fqrkhh0a0mbcgq2nv7i9m")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-blockmodeling" ,r-blockmodeling) - ("r-gplots" ,r-gplots) - ("r-testthat" ,r-testthat))) + (list r-blockmodeling r-gplots r-testthat)) (home-page "https://bioconductor.org/packages/EBSeq") (synopsis "Differential expression analysis of RNA-seq data") (description @@ -6198,32 +6586,32 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "11sgxz2xz685pgm8mf0hzm6aryx4fj5g3dlffjzpqxh3awfqa19p")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-bamsignals" ,r-bamsignals) - ("r-bezier" ,r-bezier) - ("r-biovizbase" ,r-biovizbase) - ("r-digest" ,r-digest) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-memoise" ,r-memoise) - ("r-regioner" ,r-regioner) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + "0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq")))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-bamsignals + r-bezier + r-biovizbase + r-digest + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-memoise + r-regioner + r-rsamtools + r-rtracklayer + r-s4vectors + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/karyoploteR/") (synopsis "Plot customizable linear genomes displaying arbitrary data") (description "This package creates karyotype plots of arbitrary genomes and @@ -6236,20 +6624,19 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0aw4b3p5z8ys7zlwy8s3bsqk03xwx42311yxr7q14w3f7sn3shzn")))) + "1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://r-forge.r-project.org/projects/rsymphony") (synopsis "Symphony integer linear programming solver in R") (description @@ -6266,23 +6653,20 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "0b393a8ayzbnrgkk562w1dj7avacpb3wc7yq7awiki24wi5g2lfw")))) + "0vgij5zyaw3fh7arkg4jy1mizsqzbkcsjl05mh3ng2bqh30kyqqx")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-fdrtool" ,r-fdrtool) - ("r-lpsymphony" ,r-lpsymphony) - ("r-slam" ,r-slam))) + (list r-biocgenerics r-fdrtool r-lpsymphony r-slam)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/IHW") (synopsis "Independent hypothesis weighting") (description @@ -6298,30 +6682,30 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.20.0") + (version "1.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "190rkx3sivj68in36hhin5v535yd6fvlvm7l90w1bl38zpb7p6jn")))) + "1ln8l2cp6dqg6zv7s0qnmw5ii93v5sgp0b1nwswl52zdd8mivwxy")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-limma" ,r-limma) - ("r-reshape2" ,r-reshape2) - ("r-rocr" ,r-rocr) - ("r-scales" ,r-scales) - ("r-shiny" ,r-shiny) - ("r-shinybs" ,r-shinybs) - ("r-shinydashboard" ,r-shinydashboard) - ("r-upsetr" ,r-upsetr))) + (list r-dplyr + r-dt + r-ggplot2 + r-limma + r-reshape2 + r-rocr + r-scales + r-shiny + r-shinybs + r-shinydashboard + r-upsetr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/iCOBRA") (synopsis "Comparison and visualization of ranking and assignment methods") (description @@ -6334,23 +6718,21 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "0p7va19aw0j6anx7ck879kbi5cn7dy712h5ia94adr38ssismv1v")))) + "0xsn4fm34a7xpkgmx3a1j2xzdaxf2hyla1062wqn04kw0k9y29vg")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors))) + (list r-delayedarray r-matrix r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/LTLA/ResidualMatrix") (synopsis "Create a DelayedMatrix of regression residuals") (description @@ -6365,34 +6747,34 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "1bkk69b5llkmvmpsnhymwjm2szmzypgszfsw8mak1b5ms5zf8lr0")))) + "0axkic11bwjbw8apwxx6p51s7jvlwhq7xi1bdknn54k86axq84dr")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-residualmatrix" ,r-residualmatrix) - ("r-s4vectors" ,r-s4vectors) - ("r-scaledmatrix" ,r-scaledmatrix) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-igraph + r-matrix + r-rcpp + r-residualmatrix + r-s4vectors + r-scaledmatrix + r-scuttle + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/batchelor") (synopsis "Single-Cell Batch Correction Methods") (description @@ -6408,31 +6790,31 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "1gkpagam5rap36viyr3n4psa658x9vckrxap1h67jasiiyrcfz2d")))) + "14h6giny9lhzqjsx3h7gdhsm8wfwnvp5zsl4avrflip0jmsn45yy")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-abind + r-biobase + r-biocgenerics + r-data-table + r-ggplot2 + r-plyr + r-progress + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-stringr + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/RGLab/MAST/") (synopsis "Model-based analysis of single cell transcriptomics") (description @@ -6443,48 +6825,48 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "05j1vc51f39xalggdq27y7218gkr3zq7fh7jhzsb4jj7fpn837ry")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocviews" ,r-biocviews) - ("r-cluster" ,r-cluster) - ("r-combinat" ,r-combinat) - ("r-ddrtree" ,r-ddrtree) - ("r-densityclust" ,r-densityclust) - ("r-dplyr" ,r-dplyr) - ("r-fastica" ,r-fastica) - ("r-ggplot2" ,r-ggplot2) - ("r-hsmmsinglecell" ,r-hsmmsinglecell) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-pheatmap" ,r-pheatmap) - ("r-plyr" ,r-plyr) - ("r-proxy" ,r-proxy) - ("r-qlcmatrix" ,r-qlcmatrix) - ("r-rann" ,r-rann) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rtsne" ,r-rtsne) - ("r-slam" ,r-slam) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-vgam" ,r-vgam) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + "0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85")))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-biocviews + r-cluster + r-combinat + r-ddrtree + r-densityclust + r-dplyr + r-fastica + r-ggplot2 + r-hsmmsinglecell + r-igraph + r-irlba + r-limma + r-mass + r-matrix + r-matrixstats + r-pheatmap + r-plyr + r-proxy + r-qlcmatrix + r-rann + r-rcpp + r-reshape2 + r-rtsne + r-slam + r-stringr + r-tibble + r-vgam + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/monocle") (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") (description @@ -6516,11 +6898,11 @@ qPCR data, but could be used with other types as well.") (properties `((upstream-name . "leidenbase"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (propagated-inputs - `(("r-igraph" ,r-igraph))) + (list r-igraph)) (home-page "https://github.com/cole-trapnell-lab/leidenbase") (synopsis "R and C wrappers to run the Leiden find_partition function") (description @@ -6531,6 +6913,34 @@ required source code files from the official Leidenalg distribution and several functions from the R igraph package.") (license license:gpl3+)))) +(define-public r-sanssouci + ;; sansscouci doesn't have a (versioned) release yet. + ;; This is the latest commit as of packaging for Guix. + (let ((commit "5fe20a9aaf4ac637fa83d9cc73ff1c22de97ca6f") + (revision "1")) + (package + (name "r-sanssouci") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pneuvial/sanssouci.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk")))) + (build-system r-build-system) + (propagated-inputs + (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo)) + (home-page "https://pneuvial.github.io/sanssouci") + (synopsis "Post Hoc multiple testing inference") + (description + "The goal of sansSouci is to perform post hoc inference: in a multiple +testing context, sansSouci provides statistical guarantees on possibly +user-defined and/or data-driven sets of hypotheses.") + (license license:gpl3)))) + (define-public r-monocle3 (package (name "r-monocle3") @@ -6547,50 +6957,50 @@ several functions from the R igraph package.") "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-batchelor" ,r-batchelor) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-grr" ,r-grr) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-leidenbase" ,r-leidenbase) - ("r-limma" ,r-limma) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrix-utils" ,r-matrix-utils) - ("r-pbapply" ,r-pbapply) - ("r-pbmcapply" ,r-pbmcapply) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-pryr" ,r-pryr) - ("r-proxy" ,r-proxy) - ("r-pscl" ,r-pscl) - ("r-purrr" ,r-purrr) - ("r-rann" ,r-rann) - ("r-rcpp" ,r-rcpp) - ("r-rcppparallel" ,r-rcppparallel) - ("r-reshape2" ,r-reshape2) - ("r-reticulate" ,r-reticulate) - ("r-rhpcblasctl" ,r-rhpcblasctl) - ("r-rsample" ,r-rsample) - ("r-rtsne" ,r-rtsne) - ("r-shiny" ,r-shiny) - ("r-slam" ,r-slam) - ("r-spdep" ,r-spdep) - ("r-speedglm" ,r-speedglm) - ("r-stringr" ,r-stringr) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-uwot" ,r-uwot) - ("r-viridis" ,r-viridis))) + (list r-assertthat + r-batchelor + r-biobase + r-biocgenerics + r-delayedmatrixstats + r-dplyr + r-ggplot2 + r-ggrepel + r-grr + r-htmlwidgets + r-igraph + r-irlba + r-leidenbase + r-limma + r-lmtest + r-mass + r-matrix + r-matrix-utils + r-pbapply + r-pbmcapply + r-pheatmap + r-plotly + r-pryr + r-proxy + r-pscl + r-purrr + r-rann + r-rcpp + r-rcppparallel + r-reshape2 + r-reticulate + r-rhpcblasctl + r-rsample + r-rtsne + r-shiny + r-slam + r-spdep + r-speedglm + r-stringr + r-singlecellexperiment + r-tibble + r-tidyr + r-uwot + r-viridis)) (home-page "https://github.com/cole-trapnell-lab/monocle3") (synopsis "Analysis toolkit for single-cell RNA-Seq data") (description @@ -6600,19 +7010,18 @@ several functions from the R igraph package.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "18d51dv2ygsm7kkwal341f1wrwrazyns0045j00vld367kic8jiz")))) + "0mmvzf8y4gm84hgjdpf86b1y37237wp5mc3x1g6sdiz9qi8l356v")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-matrix" ,r-matrix))) + (list r-biobase r-matrix)) (home-page "https://bioconductor.org/packages/NOISeq") (synopsis "Exploratory analysis and differential expression for RNA-seq data") (description @@ -6627,30 +7036,30 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "1dw9m3m99apmbs32461c6lnmy81n5hxbhz3p8jk419gajkh4v1ji")))) + "0gjdjkpkm9zc9hzzb6r2mknl4zyg7s2lgqppmzzhgcnvlmgvm5b5")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs - `(("r-arm" ,r-arm) - ("r-biocparallel" ,r-biocparallel) - ("r-ebseq" ,r-ebseq) - ("r-fields" ,r-fields) - ("r-ggplot2" ,r-ggplot2) - ("r-mclust" ,r-mclust) - ("r-outliers" ,r-outliers) - ("r-s4vectors" ,r-s4vectors) - ("r-scran" ,r-scran) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-arm + r-biocparallel + r-ebseq + r-fields + r-ggplot2 + r-mclust + r-outliers + r-s4vectors + r-scran + r-singlecellexperiment + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/kdkorthauer/scDD") (synopsis "Mixture modeling of single-cell RNA-seq data") (description @@ -6665,39 +7074,39 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "0zw8g4mql7b02xqwhc1i0bnhm20c1q9xqc7yz84j98pqbi996vi5")))) - (build-system r-build-system) - (propagated-inputs - `(("r-aroma-light" ,r-aroma-light) - ("r-biocparallel" ,r-biocparallel) - ("r-boot" ,r-boot) - ("r-class" ,r-class) - ("r-cluster" ,r-cluster) - ("r-compositions" ,r-compositions) - ("r-diptest" ,r-diptest) - ("r-edger" ,r-edger) - ("r-fpc" ,r-fpc) - ("r-gplots" ,r-gplots) - ("r-hexbin" ,r-hexbin) - ("r-limma" ,r-limma) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-matrixstats" ,r-matrixstats) - ("r-mixtools" ,r-mixtools) - ("r-rarpack" ,r-rarpack) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rhdf5" ,r-rhdf5) - ("r-ruvseq" ,r-ruvseq) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + "1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1")))) + (build-system r-build-system) + (propagated-inputs + (list r-aroma-light + r-biocparallel + r-boot + r-class + r-cluster + r-compositions + r-diptest + r-edger + r-fpc + r-gplots + r-hexbin + r-limma + r-matrixgenerics + r-matrixstats + r-mixtools + r-rarpack + r-rcolorbrewer + r-rhdf5 + r-ruvseq + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/scone") (synopsis "Single cell overview of normalized expression data") (description @@ -6709,27 +7118,29 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.60.0") + (version "2.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "0jhkdbcd03d5n8vn3xkad6f21xjkawyxc9rdwcj8vwc8alx730am")))) + "0plmh4x37r848g6ilvl1x8cim90rp85gikfc5m8lgi2i4xkq7hbq")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-readr" ,r-readr) - ("r-tidyr" ,r-tidyr) - ("r-xml2" ,r-xml2))) + (list r-biobase + r-data-table + r-dplyr + r-httr + r-limma + r-magrittr + r-r-utils + r-readr + r-tidyr + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/seandavi/GEOquery/") (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") (description @@ -6742,17 +7153,17 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.34.0") + (version "0.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "1sy0i3nbzsw4ymdxaiwpyx1vcg9yp3i8xfjcymqwhv95j3kyglv9")))) + "0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m")))) (build-system r-build-system) (propagated-inputs - `(("r-base64" ,r-base64))) + (list r-base64)) (home-page "https://github.com/HenrikBengtsson/illuminaio/") (synopsis "Parse Illumina microarray output files") (description @@ -6763,19 +7174,17 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "0lva0f255fcpy625frvij4n14q7nw4jcx8n2hlkxid4mgkfqwlhf")))) + "1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-multtest" ,r-multtest) - ("r-scrime" ,r-scrime))) + (list r-biobase r-multtest r-scrime)) (home-page "https://bioconductor.org/packages/siggenes/") (synopsis "Multiple testing using SAM and Efron's empirical Bayes approaches") @@ -6789,29 +7198,29 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0wi38vwfi8qr10x4xifhylxx7vfc6fqvqs649iq7lf0y7islwq2v")))) + "0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dorng" ,r-dorng) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-iterators" ,r-iterators) - ("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-matrixstats" ,r-matrixstats) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationdbi + r-biocgenerics + r-dorng + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-iterators + r-limma + r-locfit + r-matrixstats + r-s4vectors)) (home-page "https://github.com/ririzarr/bumphunter") (synopsis "Find bumps in genomic data") (description @@ -6823,47 +7232,47 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "189lzppvrz6bw2kpppawgsfjyh2ahyy8bi9z8srpas67qf2r8jmj")))) - (build-system r-build-system) - (propagated-inputs - `(("r-beanplot" ,r-beanplot) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bumphunter" ,r-bumphunter) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genefilter" ,r-genefilter) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-geoquery" ,r-geoquery) - ("r-hdf5array" ,r-hdf5array) - ("r-illuminaio" ,r-illuminaio) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-mclust" ,r-mclust) - ("r-nlme" ,r-nlme) - ("r-nor1mix" ,r-nor1mix) - ("r-preprocesscore" ,r-preprocesscore) - ("r-quadprog" ,r-quadprog) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape" ,r-reshape) - ("r-s4vectors" ,r-s4vectors) - ("r-siggenes" ,r-siggenes) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + "0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx")))) + (build-system r-build-system) + (propagated-inputs + (list r-beanplot + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bumphunter + r-data-table + r-delayedarray + r-delayedmatrixstats + r-genefilter + r-genomeinfodb + r-genomicranges + r-geoquery + r-hdf5array + r-illuminaio + r-iranges + r-lattice + r-limma + r-mass + r-mclust + r-nlme + r-nor1mix + r-preprocesscore + r-quadprog + r-rcolorbrewer + r-reshape + r-s4vectors + r-siggenes + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/hansenlab/minfi") (synopsis "Analyze Illumina Infinium DNA methylation arrays") (description @@ -6874,36 +7283,37 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.38.0") + (version "2.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "1941rc524ssx8gwhmwk40mgfrhddfs6hgldvs7bi22r29gm4y7qj")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) - ("r-genefilter" ,r-genefilter) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-illuminaio" ,r-illuminaio) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-matrixstats" ,r-matrixstats) - ("r-minfi" ,r-minfi) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + "1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka")))) + (build-system r-build-system) + (propagated-inputs + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-fdb-infiniummethylation-hg19 + r-genefilter + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-illuminaio + r-iranges + r-lattice + r-matrixstats + r-minfi + r-reshape2 + r-s4vectors + r-scales + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/methylumi") (synopsis "Handle Illumina methylation data") (description @@ -6920,31 +7330,31 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "0qjdxjdzfnnxcm07bf51v38388s5qf1i03l1sdb9jf3gxdh8yh02")))) - (build-system r-build-system) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-methylumi" ,r-methylumi) - ("r-mgcv" ,r-mgcv) - ("r-nleqslv" ,r-nleqslv) - ("r-preprocesscore" ,r-preprocesscore) - ("r-rsqlite" ,r-rsqlite))) + "0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in")))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-annotate + r-annotationdbi + r-biobase + r-dbi + r-genomicfeatures + r-genomicranges + r-kernsmooth + r-lattice + r-mass + r-methylumi + r-mgcv + r-nleqslv + r-preprocesscore + r-rsqlite)) (home-page "https://bioconductor.org/packages/lumi") (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") (description @@ -6959,37 +7369,37 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "035hrniycqadmkwg8rmzw8szv0amhy31390izy91rfrld31v2yy7")))) + "1bdnglznsfs1kdscqyjv595wiy09khcv9kxm4fmbnmksisqjz5qj")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs - `(("r-amap" ,r-amap) - ("r-apcluster" ,r-apcluster) - ("r-ellipse" ,r-ellipse) - ("r-fastcluster" ,r-fastcluster) - ("r-fpc" ,r-fpc) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-gmodels" ,r-gmodels) - ("r-igraph" ,r-igraph) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-mclust" ,r-mclust) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rtsne" ,r-rtsne) - ("r-statmod" ,r-statmod) - ("r-vegan" ,r-vegan) - ("r-zoo" ,r-zoo))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-amap + r-apcluster + r-ellipse + r-fastcluster + r-fpc + r-ggdendro + r-ggplot2 + r-gmodels + r-igraph + r-limma + r-mass + r-mclust + r-rcpp + r-rcpparmadillo + r-rtsne + r-statmod + r-vegan + r-zoo)) + (native-inputs + (list r-knitr)) (home-page "http://www.jjwanglab.org/Linnorm/") (synopsis "Linear model and normality based transformation method") (description @@ -7020,32 +7430,32 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "0fknlwdfd49v09zspg0337b0zzc8hqza3563yrw51viw3g35d6q3")))) + "1hdg446z5s616aaalzz49if1wp9nmzm2mbyva82m1vz8i7ih9m4h")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bit64" ,r-bit64) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-rhdf5" ,r-rhdf5) - ("r-shortread" ,r-shortread) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bit64 + r-dplyr + r-ggplot2 + r-magrittr + r-rhdf5 + r-shortread + r-stringr + r-tibble + r-tidyr + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/IONiseR/") (synopsis "Quality assessment tools for Oxford Nanopore MinION data") (description @@ -7072,10 +7482,7 @@ surface of a flowcell.") (properties `((upstream-name . "mutoss"))) (build-system r-build-system) (propagated-inputs - `(("r-multcomp" ,r-multcomp) - ("r-multtest" ,r-multtest) - ("r-mvtnorm" ,r-mvtnorm) - ("r-plotrix" ,r-plotrix))) + (list r-multcomp r-multtest r-mvtnorm r-plotrix)) (home-page "https://github.com/kornl/mutoss/") (synopsis "Unified multiple testing procedures") (description @@ -7100,10 +7507,7 @@ are standardized and usable by the accompanying mutossGUI package.") "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-mutoss" ,r-mutoss) - ("r-rdpack" ,r-rdpack) - ("r-tfisher" ,r-tfisher))) + (list r-lattice r-mutoss r-rdpack r-tfisher)) (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") (synopsis "Meta-analysis of significance values") (description @@ -7117,36 +7521,37 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "0fgmb309pvqf3chdhqgbd4lzhahcj5g71sica33nzn98qhipldx7")))) + "1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocparallel" ,r-biocparallel) - ("r-edger" ,r-edger) - ("r-ggplot2" ,r-ggplot2) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mgcv" ,r-mgcv) - ("r-monocle" ,r-monocle) - ("r-pbapply" ,r-pbapply) - ("r-princurve" ,r-princurve) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-slingshot" ,r-slingshot) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble) - ("r-viridis" ,r-viridis))) + (list r-biobase + r-biocparallel + r-edger + r-ggplot2 + r-igraph + r-magrittr + r-mass + r-matrix + r-matrixstats + r-mgcv + r-pbapply + r-princurve + r-rcolorbrewer + r-s4vectors + r-singlecellexperiment + r-slingshot + r-summarizedexperiment + r-tibble + r-trajectoryutils + r-viridis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://statomics.github.io/tradeSeq/index.html") (synopsis "Trajectory-based differential expression analysis") (description @@ -7173,9 +7578,7 @@ performs inference on the parameters of the GAM.") "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-yaml" ,r-yaml))) + (list r-biocgenerics r-iranges r-yaml)) (home-page "https://bioconductor.org/packages/triform/") (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") (description @@ -7187,31 +7590,31 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "1gpzrln2clfrja8rzxhsis6bi1xqglh3h2lhvqlnrx4lqxhbkv9c")))) + "0079dsgav4q03c4i0dhggc88iifd828n73kjv3sahim9akafdshl")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-variantannotation" ,r-variantannotation))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-matrix + r-rsamtools + r-rtracklayer + r-s4vectors + r-variantannotation)) (home-page "https://bioconductor.org/packages/VariantTools/") (synopsis "Tools for exploratory analysis of variant calls") (description @@ -7227,18 +7630,18 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "3.0.0") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0xwg3sxmihg3p6v3nxgrqy0nrqxi6razg3b3rjh2gcb2vv8gcqng")))) + "0yrnjrbfn8vjzvp2742lyxdqca4s18h73j44qxw7ib95x3p4lndf")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-rcolorbrewer)) (home-page "https://github.com/alexploner/Heatplus") (synopsis "Heatmaps with row and/or column covariates and colored clusters") (description @@ -7252,22 +7655,20 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "00dbgkiv9x7g2i0anzcxpycwqqqry0y7jl3ad93lhvi31qnqq1sm")))) + "15qi69kkgah7g25bymk9q1xf16hp1rd040fglg0svnydylg2d0ab")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-rcpp" ,r-rcpp))) + (list r-annotationdbi r-go-db r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/GOSemSim") (synopsis "GO-terms semantic similarity measures") (description @@ -7281,18 +7682,17 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "039bmcv5l44gszb6xapbihp3mfqdaaa8mfc05y702p78i7x93g5y")))) + "0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f")))) (build-system r-build-system) (propagated-inputs - `(("r-multtest" ,r-multtest) - ("r-qvalue" ,r-qvalue))) + (list r-multtest r-qvalue)) (home-page "https://bioconductor.org/packages/anota/") (synopsis "Analysis of translational activity") (description @@ -7312,14 +7712,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1xz5nbw5dzyah8az7mpwj8m27fsvpi2jjhfg3n27dsv8rvdncqi8")))) + "1c46m1gbgiygcj8m65h8iwzk3fkp6nynd6rk1f5qdh7kw5ap28f9")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -7331,29 +7731,62 @@ specified group of genes for a pathway has a coordinated association with a phenotype of interest.") (license license:gpl2))) +(define-public r-fcscan + (package + (name "r-fcscan") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "fcScan" version)) + (sha256 + (base32 "0b161ayq4m9xxfs0lgw632lgygzabz8gjl0n75050pa7qaazknvd")))) + (properties `((upstream-name . "fcScan"))) + (build-system r-build-system) + (propagated-inputs + (list r-doparallel + r-foreach + r-genomicranges + r-iranges + r-plyr + r-rtracklayer + r-summarizedexperiment + r-variantannotation)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/fcScan") + (synopsis "Detect clusters of coordinates with user defined options") + (description + "This package is used to detect combination of genomic coordinates +falling within a user defined window size along with user defined overlap +between identified neighboring clusters. It can be used for genomic data +where the clusters are built on a specific chromosome or specific strand. +Clustering can be performed with a \"greedy\" option allowing thus the +presence of additional sites within the allowed window size.") + (license license:artistic2.0))) + (define-public r-fgsea (package (name "r-fgsea") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "1mhdgy46nxgv7v54bk9bqfy0vgjzl1law7zy718swdd762xn6g9d")))) + "10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-biocparallel" ,r-biocparallel) - ("r-data-table" ,r-data-table) - ("r-fastmatch" ,r-fastmatch) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-bh + r-biocparallel + r-data-table + r-fastmatch + r-ggplot2 + r-gridextra + r-matrix + r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ctlab/fgsea/") (synopsis "Fast gene set enrichment analysis") (description @@ -7366,27 +7799,27 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.18.2") + (version "3.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "0kp6j42mpxrpd02cjrzqmrx3rvvpi90xiy4gc5km6ny3vxbhlaqw")))) + "10kknaqz40pb6v0fcjzp12hfpi6k5kvlqnyxx1k3y0h0wdg8hs3n")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocparallel" ,r-biocparallel) - ("r-do-db" ,r-do-db) - ("r-fgsea" ,r-fgsea) - ("r-ggplot2" ,r-ggplot2) - ("r-gosemsim" ,r-gosemsim) - ("r-qvalue" ,r-qvalue) - ("r-reshape2" ,r-reshape2))) + (list r-annotationdbi + r-biocparallel + r-do-db + r-fgsea + r-ggplot2 + r-gosemsim + r-qvalue + r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/DOSE/") (synopsis "Disease ontology semantic and enrichment analysis") (description @@ -7401,32 +7834,33 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.12.2") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "194sfmcnjfi3fvvfpljg1f80f44vvvxiij336b8z1dgzki6bqa3r")))) + "0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch")))) (build-system r-build-system) (propagated-inputs - `(("r-cowplot" ,r-cowplot) - ("r-dose" ,r-dose) - ("r-ggplot2" ,r-ggplot2) - ("r-ggraph" ,r-ggraph) - ("r-ggtree" ,r-ggtree) - ("r-gosemsim" ,r-gosemsim) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-purrr" ,r-purrr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-scatterpie" ,r-scatterpie) - ("r-shadowtext" ,r-shadowtext))) + (list r-aplot + r-dose + r-ggplot2 + r-ggraph + r-ggtree + r-gosemsim + r-igraph + r-magrittr + r-plyr + r-purrr + r-rcolorbrewer + r-reshape2 + r-scatterpie + r-shadowtext + r-yulab-utils)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/GuangchuangYu/enrichplot") (synopsis "Visualization of functional enrichment result") (description @@ -7438,33 +7872,33 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.0.5") + (version "4.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "1dccrl2ffhgmv3iqlmpln7z86ahpf0j9ma194fnknsgi3cd9rhrl")))) + "08jhcbanz24x7zdkxznxz787g0nk3jfzd7zsap13sra7qnwaswq4")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dose" ,r-dose) - ("r-downloader" ,r-downloader) - ("r-dplyr" ,r-dplyr) - ("r-enrichplot" ,r-enrichplot) - ("r-go-db" ,r-go-db) - ("r-gosemsim" ,r-gosemsim) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-qvalue" ,r-qvalue) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr) - ("r-yulab-utils" ,r-yulab-utils))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-dose + r-downloader + r-dplyr + r-enrichplot + r-go-db + r-gosemsim + r-magrittr + r-plyr + r-qvalue + r-rlang + r-tidyr + r-yulab-utils)) + (native-inputs + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") (synopsis "Analysis and visualization of functional profiles for gene clusters") (description @@ -7475,42 +7909,42 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "1fhmayciwn1m124b4dcs3gzbghgk9f7a7qmjnvvxc958cywcwkx5")))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocsingular" ,r-biocsingular) - ("r-cluster" ,r-cluster) - ("r-delayedarray" ,r-delayedarray) - ("r-edger" ,r-edger) - ("r-hdf5array" ,r-hdf5array) - ("r-howmany" ,r-howmany) - ("r-kernlab" ,r-kernlab) - ("r-limma" ,r-limma) - ("r-locfdr" ,r-locfdr) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mbkmeans" ,r-mbkmeans) - ("r-nmf" ,r-nmf) - ("r-phylobase" ,r-phylobase) - ("r-pracma" ,r-pracma) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-zinbwave" ,r-zinbwave))) + "0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc")))) + (build-system r-build-system) + (native-inputs + (list r-knitr)) + (propagated-inputs + (list r-ape + r-biocgenerics + r-biocsingular + r-cluster + r-delayedarray + r-edger + r-hdf5array + r-howmany + r-kernlab + r-limma + r-locfdr + r-matrix + r-matrixstats + r-mbkmeans + r-nmf + r-phylobase + r-pracma + r-rcolorbrewer + r-rcpp + r-s4vectors + r-scales + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-zinbwave)) (home-page "https://bioconductor.org/packages/clusterExperiment/") (synopsis "Compare clusterings for single-cell sequencing") (description "This package provides functionality for running and comparing @@ -7521,37 +7955,37 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "0ipzv7wdvfqhdyjiak956qq201igsdxm6dr6rh3dj6cssgsrnrpb")))) + "1nzy04fqwzb0ywiafgx3m3i2n1b0g4pcg8mlgh8yz5d3mmna4kag")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cluster" ,r-cluster) - ("r-fpc" ,r-fpc) - ("r-gbm" ,r-gbm) - ("r-gdata" ,r-gdata) - ("r-genefilter" ,r-genefilter) - ("r-ggvis" ,r-ggvis) - ("r-hwriter" ,r-hwriter) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-mlbench" ,r-mlbench) - ("r-pls" ,r-pls) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rpart" ,r-rpart) - ("r-sfsmisc" ,r-sfsmisc) - ("r-shiny" ,r-shiny) - ("r-threejs" ,r-threejs))) + (list r-annotate + r-biobase + r-biocgenerics + r-cluster + r-fpc + r-gbm + r-gdata + r-genefilter + r-ggvis + r-hwriter + r-magrittr + r-mass + r-mlbench + r-pls + r-rcolorbrewer + r-rcpp + r-rpart + r-sfsmisc + r-shiny + r-threejs)) (home-page "https://bioconductor.org/packages/MLInterfaces/") (synopsis "Interfaces to R machine learning procedures") (description @@ -7563,14 +7997,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.64.2") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "03y633vgxprd2abhanj4sanmb4ymz7az5aiasxn6wjzawiqjdcb1")))) + "0crj37v571005brdd0ypfx2a7d1f829xxj2hahp2gy8aj9xm4s8l")))) (build-system r-build-system) (arguments `(#:phases @@ -7580,11 +8014,7 @@ data in R and Bioconductor containers.") (substitute* "DESCRIPTION" ((", KEGG.db") ""))))))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-dbi" ,r-dbi) - ("r-go-db" ,r-go-db))) + (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db)) (home-page "https://bioconductor.org/packages/annaffy/") (synopsis "Annotation tools for Affymetrix biological metadata") (description @@ -7599,21 +8029,20 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "00fi753nsayv0xspavw8r9ni1sim8ng33hp3d3kj2b8ihygd1s10")))) + "074aa52y6c70417lxwrclk613gbs7zv3326g9ndbbzzs5pmnh1y0")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-glmnet" ,r-glmnet))) + (list r-biobase r-glmnet)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Core") (synopsis "Automated Affymetrix array analysis core package") (description @@ -7624,26 +8053,26 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "1lz85bys5dp5d1ir9c9c4wy85wkk62s14niyzzxaqrxpsji2p2iw")))) + "0q50d41n7drj5c9x6njyvzr6bj7glmkp1vpyz6cpj97j2v9nikwb")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs - `(("r-a4core" ,r-a4core) - ("r-a4preproc" ,r-a4preproc) - ("r-biobase" ,r-biobase) - ("r-glmnet" ,r-glmnet) - ("r-pamr" ,r-pamr) - ("r-rocr" ,r-rocr) - ("r-varselrf" ,r-varselrf))) + (list r-a4core + r-a4preproc + r-biobase + r-glmnet + r-pamr + r-rocr + r-varselrf)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Classif/") (synopsis "Automated Affymetrix array analysis classification package") (description @@ -7654,21 +8083,20 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "1jibm2f5glzsrvl64hxc5sf59d4w6ry0f663p619hfr44mi1mpri")))) + "1qzr54w1qys1ppd71i5b57503dijfnnbn516a2mfk5l9l7wr728d")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics))) + (list r-biobase r-biocgenerics)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Preproc/") (synopsis "Automated Affymetrix array analysis preprocessing package") (description @@ -7679,20 +8107,20 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "09jjfby5znmg2fdkhpbinx2v21zrfa44qq7cylcn9ipffqx3pk86")))) + "1vyah71gm4ngsgy0y10cdxa9b1g810gqa5pbvb3krh5i6h35smwr")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs - `(("r-xtable" ,r-xtable))) + (list r-xtable)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Reporting/") (synopsis "Automated Affymetrix array analysis reporting package") (description @@ -7703,27 +8131,27 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "101w4i0w8n7qhki22qr8l8wk8w6zalzmcywqm2g4238qv7xbnr8p")))) + "0rddxnflvbc6z4sj2h8js8yfh0zhrrwj8fk00wicaqp4rkr5yaxy")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs - `(("r-a4core" ,r-a4core) - ("r-a4preproc" ,r-a4preproc) - ("r-annaffy" ,r-annaffy) - ("r-biobase" ,r-biobase) - ("r-genefilter" ,r-genefilter) - ("r-glmnet" ,r-glmnet) - ("r-gplots" ,r-gplots) - ("r-limma" ,r-limma) - ("r-mpm" ,r-mpm) - ("r-multtest" ,r-multtest))) + (list r-a4core + r-a4preproc + r-annaffy + r-biobase + r-genefilter + r-glmnet + r-gplots + r-limma + r-mpm + r-multtest)) (home-page "https://bioconductor.org/packages/a4Base/") (synopsis "Automated Affymetrix array analysis base package") (description @@ -7734,21 +8162,17 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "0bwn185admy5k99fkd2dhhvy7x1f75r0mqn5k24dbbg0paw6nnr8")))) + "0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m")))) (build-system r-build-system) (propagated-inputs - `(("r-a4base" ,r-a4base) - ("r-a4classif" ,r-a4classif) - ("r-a4core" ,r-a4core) - ("r-a4preproc" ,r-a4preproc) - ("r-a4reporting" ,r-a4reporting))) + (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) (home-page "https://bioconductor.org/packages/a4/") (synopsis "Automated Affymetrix array analysis umbrella package") (description @@ -7759,39 +8183,39 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "1xvk84gd1lfq1icrfwwd6y79zywrisfnc3knprigzzax31aks32c")))) + "1v9g71x689ly107c0qmc5iv8qk63nn6lp7yd03jf7hlcafmvqsvz")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc))) - (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-biocstyle" ,r-biocstyle) - ("r-circlize" ,r-circlize) - ("r-flexdashboard" ,r-flexdashboard) - ("r-ggcorrplot" ,r-ggcorrplot) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-knitr" ,r-knitr) - ("r-plotly" ,r-plotly) - ("r-plyr" ,r-plyr) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-rmarkdown" ,r-rmarkdown) - ("r-stringr" ,r-stringr) - ("r-vegan" ,r-vegan) - ("r-venndiagram" ,r-venndiagram))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list pandoc)) + (propagated-inputs + (list r-biocparallel + r-biocstyle + r-circlize + r-flexdashboard + r-ggcorrplot + r-ggdendro + r-ggplot2 + r-gridextra + r-knitr + r-plotly + r-plyr + r-png + r-rcolorbrewer + r-reshape2 + r-rmarkdown + r-stringr + r-vegan + r-venndiagram)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/malhamdoosh/abseqR") (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") (description @@ -7807,21 +8231,19 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1yp0675n1g8rxdjdd7w8al5c9jq96h0kfm8218mc50z0p2fasgbj")))) + "13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc")))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-ellipse" ,r-ellipse) - ("r-ggplot2" ,r-ggplot2))) + (list r-biocparallel r-ellipse r-ggplot2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/bacon/") (synopsis "Controlling bias and inflation in association studies") (description @@ -7834,22 +8256,18 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "05drbhjqn5kik6k4h03vr3d2b6pv5rm65lsnkyx4caxxcdii4jzm")))) + "1v8xgqqv7m2kyc38x9ppwsv87ivll5ppd6z76zcxj5yspkkrqw3v")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-seqlogo" ,r-seqlogo))) + (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo)) (home-page "https://bioconductor.org/packages/rGADEM/") (synopsis "De novo sequence motif discovery") (description @@ -7871,15 +8289,15 @@ genomic sequence data.") (properties `((upstream-name . "MotIV"))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-rgadem" ,r-rgadem) - ("r-s4vectors" ,r-s4vectors))) + (list gsl)) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-genomicranges + r-iranges + r-lattice + r-rgadem + r-s4vectors)) (home-page "https://bioconductor.org/packages/MotIV/") (synopsis "Motif identification and validation") (description @@ -7892,24 +8310,24 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "04cmgg5mw1cqbg95zyfc2imykmdxyff16w26rq97xghcxwiq2b3z")))) + (base32 "0a2zg26zzk7bj5c33mbwl8dx9lh1hns8q8kwp09rbfjdichv7425")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-splitstackshape" ,r-splitstackshape))) + (list r-biocgenerics + r-biostrings + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors + r-splitstackshape)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.bioconductor.org/packages/MotifDb/") (synopsis "Annotated collection of protein-DNA binding sequence motifs") (description "This package provides more than 2000 annotated position @@ -7919,35 +8337,35 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.6.1") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "1n6v8a7c27aswmbrlcwcpghf27aplkc6nn923imglc3c0sh2lkrz")))) + (base32 "0lrgy64sv2ma6kylp4lsbwkg6ci1kn6qkk0cvzw3m4k3bgia1npj")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-grimport" ,r-grimport) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-motifdb" ,r-motifdb) - ("r-motifstack" ,r-motifstack) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tfmpvalue" ,r-tfmpvalue) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-grimport + r-gviz + r-iranges + r-matrixstats + r-motifdb + r-motifstack + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-tfmpvalue + r-variantannotation)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.bioconductor.org/packages/motifbreakR/") (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") (description "This package allows biologists to judge in the first place @@ -7970,24 +8388,20 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "0yn348kmw7v46iym913ncx4yh5nxzmba8bdys52s12ldgjja53gp")))) + "1ck6bbnrab8mbf70alfdsrcv6lq0fkvcy3klhcwyxxir7r9sgbaz")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-biostrings" ,r-biostrings) - ("r-ggplot2" ,r-ggplot2) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-xml" ,r-xml))) + (list r-ade4 r-biostrings r-ggplot2 r-htmlwidgets r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/motifStack/") (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") (description @@ -8001,33 +8415,33 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "1b8982fj0r7igj749wljsdfn3c985w8n3d5gbhr5rw73llfb8x6w")))) + "18fzi2qi95851ci7qrzwpb7v6fhwp6xi1d1vk11xbygpbvql5mls")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-biobase" ,r-biobase) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biostrings" ,r-biostrings) - ("r-delayedarray" ,r-delayedarray) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-hdf5array" ,r-hdf5array) - ("r-iranges" ,r-iranges) - ("r-rhdf5" ,r-rhdf5) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationhub + r-biobase + r-biocfilecache + r-biocgenerics + r-biocmanager + r-biostrings + r-delayedarray + r-genomeinfodb + r-genomicranges + r-hdf5array + r-iranges + r-rhdf5 + r-s4vectors + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/rcastelo/GenomicScores/") (synopsis "Work with genome-wide position-specific scores") (description @@ -8038,37 +8452,37 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "168g3xkhjzrfjpa1ynifdyfhsxx3rpyrbybsarlzr9kslw1cdkxl")))) + "0i1i3bfkp1xsjdl1nd56mlh66qz3aasd1hp09d4i31njz2f9znwn")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-chippeakanno" ,r-chippeakanno) - ("r-edger" ,r-edger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicscores" ,r-genomicscores) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-limma" ,r-limma) - ("r-motifstack" ,r-motifstack) - ("r-preseqr" ,r-preseqr) - ("r-randomforest" ,r-randomforest) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-bsgenome + r-chippeakanno + r-edger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-genomicscores + r-iranges + r-kernsmooth + r-limma + r-motifstack + r-preseqr + r-randomforest + r-rsamtools + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/ATACseqQC/") (synopsis "ATAC-seq quality control") (description @@ -8085,26 +8499,26 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "0lp2gmjlsk1yqxim5pi26i27iijw11lrcxmji7ynlag359yfnynd")))) + "08n1d03i4l2dl47axmrziiypi83yffndf0ww1b32skyjm2r0x127")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-mapplots" ,r-mapplots) - ("r-rcpp" ,r-rcpp) - ("r-vioplot" ,r-vioplot))) + (list r-annotationdbi + r-genomicranges + r-gtools + r-iranges + r-mapplots + r-rcpp + r-vioplot)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GOfuncR/") (synopsis "Gene ontology enrichment using FUNC") (description @@ -8134,25 +8548,25 @@ annotations and ontologies.") (define-public r-abaenrichment (package (name "r-abaenrichment") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 - "15v5n6d3mnj9d86swkh9agfvrsd065dldaywm1adwmkhhk525wmd")))) + "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs - `(("r-abadata" ,r-abadata) - ("r-data-table" ,r-data-table) - ("r-gofuncr" ,r-gofuncr) - ("r-gplots" ,r-gplots) - ("r-gtools" ,r-gtools) - ("r-rcpp" ,r-rcpp))) + (list r-abadata + r-data-table + r-gofuncr + r-gplots + r-gtools + r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ABAEnrichment/") (synopsis "Gene expression enrichment in human brain regions") (description @@ -8178,8 +8592,7 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.") `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dbi" ,r-dbi))) + (list r-annotationdbi r-dbi)) (home-page "https://www.iysik.com/r/annotationfuncs") (synopsis "Annotation translation functions") (description @@ -8191,18 +8604,18 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "18dd8saqx17fplvv5sbfz4p9fy7ksy3n9348rd3qlczihcrh9i3w")))) + "0grdswbf8nj0qwl0n5pqsir9242dry85j6m688j81gwwjgmzidvh")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/annotationTools/") (synopsis "Annotate microarrays and perform gene expression analyses") (description @@ -8216,39 +8629,39 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "1mn6975npncmfjlpjs3s2pgsrm32xgvnyl2vh1922l6vra97dkrc")))) + "1s6arjd0nxgxyqy7vhqcb78k0ss7vwrhv41pm346hs1nyr5dkzaq")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-gridextra" ,r-gridextra) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-nlme" ,r-nlme) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gridextra + r-gviz + r-iranges + r-lattice + r-latticeextra + r-nlme + r-rsamtools + r-s4vectors + r-seqinr + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/pappewaio/AllelicImbalance") (synopsis "Investigate allele-specific expression") (description @@ -8259,27 +8672,27 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "0qdac3qalcki20r90k40cc8d0lfywzn9pffg9d719yvs7nrsfdjr")))) + "1lclf8hkhrm6g5fp8yhvjxnwgf8p0j9ffxsmcybz4rjvmwkiz5dp")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-gseabase" ,r-gseabase) - ("r-mixtools" ,r-mixtools) - ("r-r-utils" ,r-r-utils) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-data-table + r-gseabase + r-mixtools + r-r-utils + r-s4vectors + r-shiny + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/AUCell/") (synopsis "Analysis of gene set activity in single-cell RNA-seq data") (description @@ -8298,29 +8711,29 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.34.0") + (version "4.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "1z3cxxg593d66nczz5hh2hdj1d87wc0lxrzc5sn6bp43n351q8h3")))) + "030vpn55ppfqq4408c4db4w40d17x1yq6zajb11p2glikvm1q619")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-biocgenerics" ,r-biocgenerics) - ("r-fftwtools" ,r-fftwtools) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jpeg" ,r-jpeg) - ("r-locfit" ,r-locfit) - ("r-png" ,r-png) - ("r-rcurl" ,r-rcurl) - ("r-tiff" ,r-tiff))) + (list r-abind + r-biocgenerics + r-fftwtools + r-htmltools + r-htmlwidgets + r-jpeg + r-locfit + r-png + r-rcurl + r-tiff)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/aoles/EBImage") (synopsis "Image processing and analysis toolbox for R") (description @@ -8337,28 +8750,27 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "1al615x778h17jqiyhiyf6djaq9iygs1hlbrna6y4xc0f2kvgxld")))) + "141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-ebimage" ,r-ebimage) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-matrix" ,r-matrix) - ("r-mzr" ,r-mzr) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" - ,r-summarizedexperiment))) + (list r-biocgenerics + r-data-table + r-ebimage + r-iranges + r-limma + r-matrix + r-mzr + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hansenlab/yamss") (synopsis "Tools for high-throughput metabolomics") (description @@ -8371,22 +8783,19 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "0l5271cpzjlm4m0v6xcdg2vxlbhn53x1fd59ynb9jwll93av5h1f")))) + "0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl")))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-genomicranges" ,r-genomicranges) - ("r-getoptlong" ,r-getoptlong) - ("r-iranges" ,r-iranges))) + (list r-circlize r-genomicranges r-getoptlong r-iranges)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jokergoo/gtrellis") (synopsis "Genome level Trellis layout") (description @@ -8400,33 +8809,33 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "0jr11c9hz7m49xc8pi6xrr5fhbv68vafvqpzhr0pmm51vvr1vfs9")))) + "1dxzfkvljnydv7kfybfa52dwcbkkci2r8gjspjf90k2bxf10phql")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-nmf" ,r-nmf) - ("r-pcamethods" ,r-pcamethods) - ("r-proxy" ,r-proxy) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biostrings + r-genomeinfodb + r-genomicranges + r-ggbio + r-ggplot2 + r-iranges + r-nmf + r-pcamethods + r-proxy + r-reshape2 + r-s4vectors + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/juliangehring/SomaticSignatures") (synopsis "Somatic signatures") (description @@ -8439,42 +8848,42 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.18.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "1xfkgjlm0rxz82qcaqzx95cwirxifd9dsswjg3zcqmz03v7a0gz2")))) + "08r05fzpraggbxv15lx0b68kjlkysp0rcdlm6n9avzmlsdqplb2h")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-circlize" ,r-circlize) - ("r-complexheatmap" ,r-complexheatmap) - ("r-corrplot" ,r-corrplot) - ("r-dendextend" ,r-dendextend) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-getoptlong" ,r-getoptlong) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtrellis" ,r-gtrellis) - ("r-keggrest" ,r-keggrest) - ("r-limsolve" ,r-limsolve) - ("r-magrittr" ,r-magrittr) - ("r-pmcmr" ,r-pmcmr) - ("r-pracma" ,r-pracma) - ("r-reshape2" ,r-reshape2) - ("r-somaticsignatures" ,r-somaticsignatures) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biostrings + r-bsgenome-hsapiens-ucsc-hg19 + r-circlize + r-complexheatmap + r-corrplot + r-dendextend + r-doparallel + r-dplyr + r-genomeinfodb + r-genomicranges + r-getoptlong + r-ggbeeswarm + r-ggplot2 + r-gridextra + r-gtrellis + r-keggrest + r-limsolve + r-magrittr + r-pmcmrplus + r-pracma + r-reshape2 + r-somaticsignatures + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/YAPSA/") (synopsis "Yet another package for signature analysis") (description @@ -8488,22 +8897,22 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "1z4abw9s2hs3csnx25nli7fpvb3rh3l0swzl0wfqp087fcs78pxi")))) + "0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-biostrings" ,r-biostrings) - ("r-xvector" ,r-xvector))) + (list r-affy + r-affyio + r-biobase + r-biocmanager + r-biostrings + r-xvector)) (home-page "https://bioconductor.org/packages/gcrma/") (synopsis "Background adjustment using sequence information") (description @@ -8534,11 +8943,7 @@ gene-specific binding is expected.") "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-gcrma" ,r-gcrma) - ("r-genefilter" ,r-genefilter))) + (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter)) (home-page "https://bioconductor.org/packages/simpleaffy/") (synopsis "Very simple high level analysis of Affymetrix data") (description @@ -8562,7 +8967,7 @@ generating high resolution journal figures.") "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96")))) (build-system r-build-system) (propagated-inputs - `(("r-simpleaffy" ,r-simpleaffy))) + (list r-simpleaffy)) (home-page "https://bioconductor.org/packages/yaqcaffy/") (synopsis "Affymetrix quality control and reproducibility analysis") (description @@ -8574,25 +8979,25 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "1fkma2ic448h2lrlza8ipg65gpfsz4fhlxcnjpmzhhmzp2xi2p4a")))) + "1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-minfi" ,r-minfi) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-biobase + r-doparallel + r-foreach + r-ggplot2 + r-iterators + r-minfi + r-rcolorbrewer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/quantro/") (synopsis "Test for when to use quantile normalization") (description @@ -8607,29 +9012,29 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "1x07l255x52z6cgdc2j8285shqszhr034xm5686rp6d35vah55ji")))) + "0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biomart" ,r-biomart) - ("r-downloader" ,r-downloader) - ("r-edger" ,r-edger) - ("r-gplots" ,r-gplots) - ("r-limma" ,r-limma) - ("r-matrixstats" ,r-matrixstats) - ("r-preprocesscore" ,r-preprocesscore) - ("r-quantro" ,r-quantro) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-readr" ,r-readr))) + (list r-biobase + r-biomart + r-downloader + r-edger + r-gplots + r-limma + r-matrixstats + r-preprocesscore + r-quantro + r-rcolorbrewer + r-readr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/yarn/") (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") (description @@ -8644,24 +9049,24 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0vp0n90rvjm8rzwkbrxa3fasb9val56bz2srz72xwsl3jzb5yk6w")))) + "0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors + r-summarizedexperiment)) (home-page "https://github.com/vodkatad/roar/") (synopsis "Identify differential APA usage from RNA-seq alignments") (description @@ -8684,17 +9089,17 @@ sites and alignments obtained from standard RNA-seq experiments.") (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-locfit" ,r-locfit) - ("r-magrittr" ,r-magrittr) - ("r-matrixstats" ,r-matrixstats) - ("r-pracma" ,r-pracma) - ("r-roar" ,r-roar))) + (list r-biobase + r-deseq2 + r-dplyr + r-ggplot2 + r-locfit + r-magrittr + r-matrixstats + r-pracma + r-roar)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Liuy12/XBSeq") (synopsis "Test for differential expression for RNA-seq data") (description @@ -8712,19 +9117,19 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "1cs32sig1yvqn9xs0cvhfpmkh2lbllx7aab80sz58x03wnx8v60z")))) + "1icqyxkx5a9y3wahkxpxngw85c7l4hih1ym9nwwn9qy93pnw1zi4")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) (propagated-inputs - `(("r-waveslim" ,r-waveslim))) + (list r-waveslim)) (home-page "https://bioconductor.org/packages/MassSpecWavelet/") (synopsis "Mass spectrum processing by wavelet-based algorithms") (description @@ -8736,34 +9141,35 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.14.1") + (version "3.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "1g8k90p0sbcb3rdrbldj5bcjp2piy5ldni4jplyr78vjpmrmvqk7")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-massspecwavelet" ,r-massspecwavelet) - ("r-mscoreutils" ,r-mscoreutils) - ("r-msnbase" ,r-msnbase) - ("r-mzr" ,r-mzr) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-rann" ,r-rann) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-robustbase" ,r-robustbase) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + "19kjyi6br9qp2pnp24shgbww3iqaaqxk9791w8w8qbd6sxijd143")))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-biocparallel + r-iranges + r-lattice + r-massspecwavelet + r-mscoreutils + r-msfeatures + r-msnbase + r-mzr + r-plyr + r-protgenerics + r-rann + r-rcolorbrewer + r-robustbase + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/xcms/") (synopsis "LC/MS and GC/MS mass spectrometry data analysis") (description @@ -8776,22 +9182,20 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wrench (package (name "r-wrench") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "0yssmqayaryrc0asjjqxdipqdfg309llrzldx38jrfgdsza6bvs0")))) + "1vzv7sswijgb8nq58yrc19wlw2nnpjvans86fqqzs4p8wvq8j06n")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-matrixstats" ,r-matrixstats))) + (list r-limma r-locfit r-matrixstats)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/HCBravoLab/Wrench") (synopsis "Wrench normalization for sparse count data") (description @@ -8802,28 +9206,28 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "13f3g6fcc29k0g21mhnypm3nc6qqjw867vamvfkdzynspsfb32ga")))) + "01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-purrr" ,r-purrr) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-assertthat + r-cowplot + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-purrr + r-rtracklayer + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/wiggleplotr/") (synopsis "Make read coverage plots from BigWig files") (description @@ -8836,14 +9240,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "186xgpgyfyi4angxhz6558lfpzvvszzlpyfr8xnbccs3gshk3db2")))) + "0jajfh78116wjfwbmzfvcbxswai4jj9ypzmfhs5j5iypaf8zff8j")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -8857,27 +9261,26 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1mpdw477j78s2nvlf2lzm6mdjcpamyyazjn060h9q3apawn6zajx")))) + "1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17")))) (build-system r-build-system) (inputs - `(("netpbm" ,netpbm) - ("perl" ,perl))) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-annaffy" ,r-annaffy) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-gcrma" ,r-gcrma) - ("r-multtest" ,r-multtest) - ("r-qvalue" ,r-qvalue) - ("r-vsn" ,r-vsn))) + (list netpbm perl)) + (propagated-inputs + (list r-affy + r-annaffy + r-biobase + r-biocmanager + r-gcrma + r-multtest + r-qvalue + r-vsn)) (home-page "https://www.bioconductor.org/") (synopsis "Bioconductor web interface") (description @@ -8890,25 +9293,25 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "1y8krazz2qdn0wn8ijjs2gn5dl5l960v6bijbkvh0r8066l7viky")))) + "05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq")))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-edger" ,r-edger) - ("r-genefilter" ,r-genefilter) - ("r-matrix" ,r-matrix) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-softimpute" ,r-softimpute) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocparallel + r-edger + r-genefilter + r-matrix + r-singlecellexperiment + r-softimpute + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/zinbwave") (synopsis "Zero-inflated negative binomial model for RNA-seq data") (description "This package implements a general and flexible zero-inflated @@ -8923,24 +9326,20 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1k7xaxr2gn26y8bps5l32g2axfhdn07nbk4q3qcx32d5jm75qkx2")))) + "0fk05vrmyyrhmkwi06lsi553mlpqj3fgwhk1kygz83iqv5z2vfw9")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr))) + (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ronammar/zFPKM/") (synopsis "Functions to facilitate zFPKM transformations") (description @@ -8952,20 +9351,22 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "1.14.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "0r5yqjal48xlcv5cidi7p3zwygvsllmv2zzkwkc9kfq083l2i4ih")))) + "0xpvrx2ak9x913sym4l46ycwbnmpcdwb3bf3dfd2gsp0krv8vh1x")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) + (propagated-inputs + (list r-magrittr r-rsamtools)) (inputs - `(("zlib" ,zlib))) + (list samtools zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/Rbowtie2/") (synopsis "R wrapper for Bowtie2 and AdapterRemoval") (description @@ -8977,24 +9378,24 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "10vpjvl4wps857xiy8rpzr82jzdfbc5rgwh3ir3my26lfws4hfz8")))) + "0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gridextra" ,r-gridextra) - ("r-tidyr" ,r-tidyr))) + (list r-biobase + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/saezlab/progeny") (synopsis "Pathway responsive gene activity inference") (description @@ -9007,18 +9408,18 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "0ni3vblcadhwxaq1pf1n9jn66cp3bqch68ww4c8zh19zagil2y7r")))) + "1ryqr3mpakjml0jhbk28k2z511sdl87wxdczxq1rwx98s0pc9mnh")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) - (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) + (propagated-inputs (list r-arrmdata)) (home-page "https://bioconductor.org/packages/ARRmNormalization/") (synopsis "Adaptive robust regression normalization for methylation data") (description @@ -9030,27 +9431,27 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "0ymg4hmabk233qgassld62achjylm12rnidxbakfkx4dvvlbhxxv")))) + "11qayqmgv274hc4h1v222sma07wkxjm8002fl6w3yvi225zq1qc1")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-dbplyr" ,r-dbplyr) - ("r-dplyr" ,r-dplyr) - ("r-filelock" ,r-filelock) - ("r-httr" ,r-httr) - ("r-rappdirs" ,r-rappdirs) - ("r-rsqlite" ,r-rsqlite))) + (list r-curl + r-dbi + r-dbplyr + r-dplyr + r-filelock + r-httr + r-rappdirs + r-rsqlite)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocFileCache/") (synopsis "Manage files across sessions") (description @@ -9063,17 +9464,17 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "1haj25c4cmmjjvh181b41a9pvkh92f7k2w4ljn17iqg31vm45za1")))) + "0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://bioconductor.org/packages/iClusterPlus/") (synopsis "Integrative clustering of multi-type genomic data") (description @@ -9093,20 +9494,19 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "0mfikbrs28q7r3lnsq0jma5x6nkrnm3q46242jh35w9c969jk5yy")))) + "0ardmryx6ac7v6n900a1klrrldvbmh7bxvy8ldz8rwid19h29ikr")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) + (inputs (list zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/Rbowtie/") (synopsis "R bowtie wrapper") (description @@ -9118,33 +9518,33 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "0i1yaw8h8gibakvaf1xd6nnjx2bsb2s9c0q74rbq9lm7haihivp6")))) + "15l0r6svs27k82dd472is26shwayz6rs5ylg5gpf3mldr7sa5kja")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-runit" ,r-runit) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-igraph + r-iranges + r-rsamtools + r-rtracklayer + r-runit + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/SGSeq/") (synopsis "Splice event prediction and quantification from RNA-seq data") (description @@ -9161,14 +9561,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "1hqahh5h22mj2crqp6r9xnm111xmfgk39c100rcaziqrpdy5npk8")))) + "092rws9vjxgm2jpkbp6ign47zmillyyidnc7ylcbn4zr9j5lwv0y")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments @@ -9184,11 +9584,9 @@ interpretation.") (("^CPP =.*") (which "g++"))) #t))))) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-sgseq" ,r-sgseq))) + (list r-genomicfeatures r-genomicranges r-sgseq)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/fmicompbio/Rhisat2") (synopsis "R Wrapper for HISAT2 sequence aligner") (description @@ -9201,37 +9599,36 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "1635ff11ahzjrh3cdcxrq5bgd100n444k7mc0maz0jx21vj8qqb1")))) + "0d292xgaq8d3cdpa9anabda03lis46xc29iw9c5k5i3sj7dcr4g5")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rbowtie" ,r-rbowtie) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicfeatures + r-genomicfiles + r-genomicranges + r-iranges + r-rbowtie + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-shortread)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/QuasR/") (synopsis "Quantify and annotate short reads in R") (description @@ -9244,37 +9641,37 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "02hwj2vd003x0zf273ndnwh7kxy6wc3sz14d3kryp2w2aqjj826f")))) + "0hcxkrfja0gmd8r2llijdvaw2xiiplk037305inimz0qna6w2071")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biocstyle" ,r-biocstyle) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfiles" ,r-genomicfiles) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-knitr" ,r-knitr) - ("r-markdown" ,r-markdown) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-biocstyle + r-biostrings + r-biovizbase + r-genomicalignments + r-genomicfiles + r-ggplot2 + r-iranges + r-knitr + r-markdown + r-plyr + r-rcpp + r-reshape2 + r-rsamtools + r-s4vectors + r-shiny + r-shortread)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/labbcb/Rqc") (synopsis "Quality control tool for high-throughput sequencing data") (description @@ -9287,21 +9684,18 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.24.0") + (version "3.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "0p6mr67mkw54490sv4dvkyh8l0xkpjfbqy532vi8l41i40qg3gry")))) + "0ki4rcwjgbixzy5q9s30ajx5zhpl18q50znrb60fchvl4hj9h93w")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-slam" ,r-slam) - ("r-tsne" ,r-tsne))) + (list r-igraph r-matrix r-slam r-tsne)) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description @@ -9326,9 +9720,7 @@ routines to analyse the resulting networks and their natural projections.") "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass))) + (list r-biobase r-limma r-mass)) (home-page "https://bioconductor.org/packages/birta") (synopsis "Bayesian inference of regulation of transcriptional activity") (description @@ -9345,29 +9737,29 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "1hyk40xgmy50rqxwdvc64d3pgz5vsg8vmlj5cp5m0n5m0adxcdfj")))) + "17asldnxqvp3sijx7nbi2lbbgnq4iq8z72qlg9080sm5lga1yy1s")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-qqman" ,r-qqman) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biobase + r-biocgenerics + r-genomicranges + r-ggplot2 + r-ggrepel + r-iranges + r-limma + r-qqman + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/MultiDataSet/") (synopsis "Implementation of MultiDataSet and ResultSet") (description @@ -9382,20 +9774,19 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "1j99kdywyljqzdcns5ysh590w4w8iiwzpddpfk5c8d4whax7vk5b")))) + "0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-multidataset" ,r-multidataset))) + (list r-biobase r-multidataset)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") (synopsis "Multivariate analysis and feature selection of omics data") (description @@ -9420,23 +9811,19 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "159fbkymn92li7dinsm56nsacjp8wnhsljv7airgs9m82p8wd5sl")))) + "189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-e1071" ,r-e1071) - ("r-multidataset" ,r-multidataset) - ("r-randomforest" ,r-randomforest) - ("r-ropls" ,r-ropls))) + (list r-biobase r-e1071 r-multidataset r-randomforest r-ropls)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/biosigner/") (synopsis "Signature discovery from omics data") (description @@ -9453,31 +9840,31 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1ls1qdfppcxysggi3bghrnspb5a3s40pm2mj4x0whc7c40cf90mg")))) + "1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-readr" ,r-readr) - ("r-regioner" ,r-regioner) - ("r-reshape2" ,r-reshape2) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationdbi + r-annotationhub + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-readr + r-regioner + r-reshape2 + r-rtracklayer + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/annotatr/") (synopsis "Annotation of genomic regions to genomic annotations") (description @@ -9494,19 +9881,19 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.6.4") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "043m4512q73x6q529hqfgrap0fq5anvny4va085nafia06b805pi")))) + "0lpx0dp5570kbrq7v0g573axkhi00qrf38si59vmvnqxhmkvsixn")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (home-page "https://bioconductor.org/packages/Rsubread/") (synopsis "Subread sequence alignment and counting for R") (description @@ -9520,23 +9907,23 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "1sdwgyvrsz0pp60zdfrcgb7bs8s87j7257p8ck813ydizc324x9w")))) + "0rgybkzbn8c3kpbz0ddghp1np0gka0cgiqvkk5jbnhlgf4s07161")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-corpcor" ,r-corpcor) - ("r-flowcore" ,r-flowcore) - ("r-graph" ,r-graph) - ("r-runit" ,r-runit) - ("r-xml" ,r-xml))) + (list r-biobase + r-corpcor + r-flowcore + r-graph + r-runit + r-xml)) (home-page "https://github.com/jspidlen/flowUtils") (synopsis "Utilities for flow cytometry") (description @@ -9546,21 +9933,19 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "163nr50nyvwrsajmm0cgxp70pqk61mgw0k7ams694hcb42162j8b")))) + "13z43qbk9z7mvy8v8k185m6n020i6ahb18pm4q88rs75qlklzdkr")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) (propagated-inputs - `(("r-all" ,r-all) - ("r-biobase" ,r-biobase) - ("r-cluster" ,r-cluster))) + (list r-all r-biobase r-cluster)) (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") (synopsis "Clustering algorithm") (description @@ -9571,25 +9956,25 @@ cluster count and membership by stability evidence in unsupervised analysis.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.4.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "0wl7zqwv0i38dfzqfsz40n3mcbxi38ffn1rbd5pm9s7hq16zr4nv")))) + "16m5w6cp28p4fs2p8c8rjcg1d686xl8mpas816i7zxfh8m0bcqc9")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rprotobuflib" ,r-rprotobuflib))) + (list r-bh + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rhdf5lib + r-rprotobuflib)) (home-page "https://bioconductor.org/packages/cytolib/") (synopsis "C++ infrastructure for working with gated cytometry") (description @@ -9600,28 +9985,28 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "13xpbkxi53rxmhvpdiy6bydmhicmxd2gi96d9c1qx4lkss2f14nc")))) + "0zbd2hrdbb6r0np6nd3ab8nlcf9l57vcwnnhbqkbas8y0c2i2mwp")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cytolib" ,r-cytolib) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rprotobuflib" ,r-rprotobuflib) - ("r-s4vectors" ,r-s4vectors))) + (list r-bh + r-biobase + r-biocgenerics + r-cytolib + r-matrixstats + r-rcpp + r-rcpparmadillo + r-rprotobuflib + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description @@ -9632,21 +10017,18 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "1awskkq48qhv4v9glxgfqi0kgwqd62fbj641k4vvxfcwsf2c7bfg")))) + "0iy8hvi0inj1ylhdx6q4mya9k55iazprz6fdrnq1mxb2iyndzsl6")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-feature" ,r-feature) - ("r-flowcore" ,r-flowcore) - ("r-rrcov" ,r-rrcov))) + (list r-biobase r-feature r-flowcore r-rrcov)) (home-page "https://bioconductor.org/packages/flowMeans") (synopsis "Non-parametric flow cytometry data gating") (description @@ -9658,27 +10040,27 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "1lm88qnfv6rnnr7wmgbvwyj272imjjjn7h3agxqqzsbmn8vyrnf0")))) + "1c6wb2x24ydqp5nxrx6bhj6f13x9djfy9awkc7zn63xkag7mvvar")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-flowcore" ,r-flowcore) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-bh + r-biobase + r-biocgenerics + r-flowcore + r-rcpp + r-rcpparmadillo + r-rhdf5lib + r-zlibbioc)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ncdfFlow/") (synopsis "HDF5 based storage for flow cytometry data") (description @@ -9689,30 +10071,30 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0jd6m84m4znnpix4bcgdby7mnflsn206f5x2vw9n8rxnwzx77wpg")))) + "17dnmsa92gc2za36c3klgd7rklqlxrhkzs5ksnrc1am6a4knc0p1")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-flowcore" ,r-flowcore) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-hexbin" ,r-hexbin) - ("r-ncdfflow" ,r-ncdfflow) - ("r-plyr" ,r-plyr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) + (list r-data-table + r-flowcore + r-flowworkspace + r-ggplot2 + r-gridextra + r-hexbin + r-ncdfflow + r-plyr + r-rcolorbrewer + r-rlang + r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/RGLab/ggcyto/issues") (synopsis "Visualize Cytometry data with ggplot") (description @@ -9726,28 +10108,28 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "17x04xwyw2pp5zkhgvrmxkb8cbrv9wql6xhjsfpq0n6yd9dxqc1v")))) + "039sh7qn25gp2b34khs8dyrdpxyapsjlprrvxlz8f7dl8gmggl04")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-flowcore" ,r-flowcore) - ("r-hexbin" ,r-hexbin) - ("r-idpmisc" ,r-idpmisc) - ("r-kernsmooth" ,r-kernsmooth) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-mass" ,r-mass) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-biobase + r-flowcore + r-hexbin + r-idpmisc + r-kernsmooth + r-lattice + r-latticeextra + r-mass + r-rcolorbrewer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/flowViz/") (synopsis "Visualization for flow cytometry") (description @@ -9757,34 +10139,33 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.30.0") + (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "03xsmprrkxwkaksjlaxwp54mqfb3zlg6dbqhp87w78fwscisv76b")))) + "0ch7mkq40qcnxwgzy51vjdlwyzx4bvp03vpdm6dwjc6qy8a6qfzi")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments `(#:configure-flags (list "--configure-args=--enable-bundled-gsl=no"))) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-clue" ,r-clue) - ("r-corpcor" ,r-corpcor) - ("r-ellipse" ,r-ellipse) - ("r-flowcore" ,r-flowcore) - ("r-flowviz" ,r-flowviz) - ("r-graph" ,r-graph) - ("r-mnormt" ,r-mnormt))) + (list r-biobase + r-biocgenerics + r-clue + r-corpcor + r-ellipse + r-flowcore + r-flowviz + r-graph + r-mnormt)) (inputs - `(("gsl" ,gsl))) + (list gsl)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://bioconductor.org/packages/flowClust") (synopsis "Clustering for flow cytometry") (description @@ -9797,14 +10178,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "1hyds97ay4mn7nl830yh9v8mlasgsljsx5wsrhz2zsmbbyx6wbnb")))) + "04qlhbhdchpr35rdc6jc3y8fy6znnfrdlsb8am04agbrvpjgrx10")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -9815,7 +10196,7 @@ model with Box-Cox transformation.") (with-directory-excursion "src" (invoke "tar" "xf" "protobuf-3.13.0.tar.gz"))))))) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/RProtoBufLib/") (synopsis "C++ headers and static libraries of Protocol buffers") (description @@ -9826,46 +10207,46 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.4.0") + (version "4.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "1a9qb2dcvwgb3z0vdbbzn1rzy77d3da72kirs272344hdx9b2cx9")))) + "11ni7kgk9s1fz3lvg85s6r7x2fhk4m7cdpilji05ya12jsyr3fig")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs - `(("r-aws-s3" ,r-aws-s3) - ("r-aws-signature" ,r-aws-signature) - ("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cytolib" ,r-cytolib) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-flowcore" ,r-flowcore) - ("r-ggplot2" ,r-ggplot2) - ("r-graph" ,r-graph) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-matrixstats" ,r-matrixstats) - ("r-ncdfflow" ,r-ncdfflow) - ("r-rbgl" ,r-rbgl) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rprotobuflib" ,r-rprotobuflib) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-aws-s3 + r-aws-signature + r-bh + r-biobase + r-biocgenerics + r-cytolib + r-data-table + r-delayedarray + r-digest + r-dplyr + r-flowcore + r-ggplot2 + r-graph + r-lattice + r-latticeextra + r-matrixstats + r-ncdfflow + r-rbgl + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rgraphviz + r-rhdf5lib + r-rprotobuflib + r-s4vectors + r-scales + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/flowWorkspace/") (synopsis "Infrastructure for working with cytometry data") (description @@ -9880,31 +10261,31 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.4.0") + (version "4.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1yr5m7qmhmm52c70z3d0zy4zgf0hja7r2ig9yljv5w86bzm962x6")))) + "0jjfq66m4lbpkynwxaparkd05znhp3jl9ccj37gyghly294x3rm9")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cluster" ,r-cluster) - ("r-fda" ,r-fda) - ("r-flowcore" ,r-flowcore) - ("r-flowviz" ,r-flowviz) - ("r-flowworkspace" ,r-flowworkspace) - ("r-kernsmooth" ,r-kernsmooth) - ("r-ks" ,r-ks) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-ncdfflow" ,r-ncdfflow) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rrcov" ,r-rrcov))) + (list r-biobase + r-biocgenerics + r-cluster + r-fda + r-flowcore + r-flowviz + r-flowworkspace + r-kernsmooth + r-ks + r-lattice + r-mass + r-ncdfflow + r-rcolorbrewer + r-rrcov)) (home-page "http://www.github.com/RGLab/flowStats") (synopsis "Statistical methods for the analysis of flow cytometry data") (description @@ -9916,40 +10297,40 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "1par1d5pk1rjg15q7i5z5wqma7xg6fycb826a823wk8wr52a885x")))) + "11svr1lk383pkm4npwrnf3h37b3drjsmcwcgdbb45x8k2k95z2fm")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-clue" ,r-clue) - ("r-data-table" ,r-data-table) - ("r-flowclust" ,r-flowclust) - ("r-flowcore" ,r-flowcore) - ("r-flowstats" ,r-flowstats) - ("r-flowviz" ,r-flowviz) - ("r-flowworkspace" ,r-flowworkspace) - ("r-graph" ,r-graph) - ("r-gtools" ,r-gtools) - ("r-ks" ,r-ks) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-ncdfflow" ,r-ncdfflow) - ("r-plyr" ,r-plyr) - ("r-r-utils" ,r-r-utils) - ("r-rbgl" ,r-rbgl) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rrcov" ,r-rrcov))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-clue + r-data-table + r-flowclust + r-flowcore + r-flowstats + r-flowviz + r-flowworkspace + r-graph + r-gtools + r-ks + r-lattice + r-mass + r-ncdfflow + r-plyr + r-r-utils + r-rbgl + r-rcolorbrewer + r-rcpp + r-rrcov)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description @@ -9960,49 +10341,48 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "0ixy7mmnipk8wy61wz6qy7jfbc5zhs6p5iqaii8hdprjnb841ri7")))) + "16rgsc2dz5b8lm3ma8nh9wiknrdnvfjcsij7809rmcfs0gn1arcz")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs - `(("libxml2" ,libxml2) - ("zlib" ,zlib))) - (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-corpcor" ,r-corpcor) - ("r-cytolib" ,r-cytolib) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-flowcore" ,r-flowcore) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggcyto" ,r-ggcyto) - ("r-graph" ,r-graph) - ("r-jsonlite" ,r-jsonlite) - ("r-lattice" ,r-lattice) - ("r-opencyto" ,r-opencyto) - ("r-plyr" ,r-plyr) - ("r-rbgl" ,r-rbgl) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rprotobuflib" ,r-rprotobuflib) - ("r-runit" ,r-runit) - ("r-tibble" ,r-tibble) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list libxml2 zlib)) + (propagated-inputs + (list r-base64enc + r-bh + r-biobase + r-corpcor + r-cytolib + r-data-table + r-dplyr + r-flowcore + r-flowworkspace + r-ggcyto + r-graph + r-jsonlite + r-lattice + r-opencyto + r-plyr + r-rbgl + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rgraphviz + r-rhdf5lib + r-rprotobuflib + r-runit + r-tibble + r-xml + r-xml2 + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/RGLab/CytoML") (synopsis "GatingML interface for cross platform cytometry data sharing") (description @@ -10013,39 +10393,39 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "18h7p7g3w9imyd1c93jllgp4kd74z96cs85wcqfhmd26nx18hl82")))) + "062xrv8li2z849qa8mv5dhafqli6ziz099ikjfvi7v2fr7174p8f")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-colorramps" ,r-colorramps) - ("r-consensusclusterplus" ,r-consensusclusterplus) - ("r-cytoml" ,r-cytoml) - ("r-dplyr" ,r-dplyr) - ("r-flowcore" ,r-flowcore) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggforce" ,r-ggforce) - ("r-ggnewscale" ,r-ggnewscale) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpointdensity" ,r-ggpointdensity) - ("r-ggpubr" ,r-ggpubr) - ("r-ggrepel" ,r-ggrepel) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-pheatmap" ,r-pheatmap) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rtsne" ,r-rtsne) - ("r-scattermore" ,r-scattermore) - ("r-tidyr" ,r-tidyr) - ("r-xml" ,r-xml))) + (list r-biocgenerics + r-colorramps + r-consensusclusterplus + r-cytoml + r-dplyr + r-flowcore + r-flowworkspace + r-ggforce + r-ggnewscale + r-ggplot2 + r-ggpointdensity + r-ggpubr + r-ggrepel + r-igraph + r-magrittr + r-pheatmap + r-rcolorbrewer + r-rlang + r-rtsne + r-scattermore + r-tidyr + r-xml)) (home-page "https://bioconductor.org/packages/FlowSOM/") (synopsis "Visualize and interpret cytometry data") (description @@ -10056,34 +10436,34 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.16.3") + (version "6.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "1x6dbw4q6p9vngm256fr96r9fjxk5nik5ivkhbl5a9zqyq8wagpa")))) + "1wpskrnl2bry9m4k2djhjddcd8gpwf51gp5c3si1y7qxja78ql9f")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-corpcor" ,r-corpcor) - ("r-dplyr" ,r-dplyr) - ("r-ellipse" ,r-ellipse) - ("r-ggrepel" ,r-ggrepel) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-igraph" ,r-igraph) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats) - ("r-rarpack" ,r-rarpack) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-corpcor + r-dplyr + r-ellipse + r-ggrepel + r-ggplot2 + r-gridextra + r-igraph + r-lattice + r-mass + r-matrixstats + r-rarpack + r-rcolorbrewer + r-reshape2 + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "http://www.mixOmics.org") (synopsis "Multivariate methods for exploration of biological datasets") (description @@ -10102,36 +10482,36 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "04vxc43p3kpsx0vksk2nwmy9p56h35z2mc8j9p2wm29zaz1y8j3p")))) + "1500jivij7zdycdd0i0b7mgp44w4z0hqnpzqbq8nhvzzdigic8x9")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs - `(("r-beanplot" ,r-beanplot) - ("r-dosnow" ,r-dosnow) - ("r-dplyr" ,r-dplyr) - ("r-fnn" ,r-fnn) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-gmodels" ,r-gmodels) - ("r-gplots" ,r-gplots) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats) - ("r-mixomics" ,r-mixomics) - ("r-moments" ,r-moments) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-reshape2" ,r-reshape2) - ("r-robustbase" ,r-robustbase) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beanplot + r-dosnow + r-dplyr + r-fnn + r-foreach + r-ggplot2 + r-gmodels + r-gplots + r-mass + r-matrixstats + r-mixomics + r-moments + r-rcpp + r-rcppeigen + r-reshape2 + r-robustbase + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/DepecheR/") (synopsis "Identify traits of clusters in high-dimensional entities") (description @@ -10148,31 +10528,31 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1yh0l11vnslgr6zsbpgc8mc4aa32zy34f5yrz98hkcdl53iw5y7f")))) + "1qarr7xd71kz1haccj65x7sc7pc4v6xpqcfa3rkyp2bk240gigi7")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs - `(("r-arrow" ,r-arrow) - ("r-aucell" ,r-aucell) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-feather" ,r-feather) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gseabase" ,r-gseabase) - ("r-r-utils" ,r-r-utils) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-arrow + r-aucell + r-biocgenerics + r-data-table + r-dplyr + r-feather + r-genomeinfodb + r-genomicranges + r-gseabase + r-r-utils + r-summarizedexperiment + r-tibble)) + (native-inputs + (list r-knitr)) (home-page "https://aertslab.org/#scenic") (synopsis "Identify transcription factor binding motifs enriched on a gene list") (description @@ -10190,23 +10570,19 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-chicago (package (name "r-chicago") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "0dkwy6pfvzd7g4qmhjl24ypn92l78w1zy0ajhcxgg39f7zsq883x")))) + "0nz9v37p7zl8yw3ykdbsb3izcwgx349wvrhwfyyn9h3jxjfafngn")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-delaporte" ,r-delaporte) - ("r-hmisc" ,r-hmisc) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Chicago") (synopsis "Capture Hi-C analysis of genomic organization") (description @@ -10216,40 +10592,40 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "1y34cm52bv1v2hr7sz8zjzxwd4wng7v75avz5wx45l0ld54z9l10")))) - (build-system r-build-system) - (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-fnn" ,r-fnn) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-glasso" ,r-glasso) - ("r-gviz" ,r-gviz) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-monocle" ,r-monocle) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vgam" ,r-vgam))) - (native-inputs - `(("r-knitr" ,r-knitr))) + "1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7")))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-biobase + r-biocgenerics + r-data-table + r-dplyr + r-fnn + r-genomicranges + r-ggplot2 + r-glasso + r-gviz + r-igraph + r-iranges + r-matrix + r-monocle + r-plyr + r-reshape2 + r-s4vectors + r-stringi + r-stringr + r-tibble + r-tidyr + r-vgam)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/cicero/") (synopsis "Predict cis-co-accessibility from single-cell data") (description @@ -10276,50 +10652,50 @@ accessibility data.") (base32 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) (propagated-inputs - `(("r-monocle3" ,r-monocle3) - ,@(alist-delete "r-monocle" - (package-propagated-inputs r-cicero))))))) + (modify-inputs (package-propagated-inputs r-cicero) + (delete "r-monocle") + (prepend r-monocle3)))))) (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "1hif40vfg2lkbyf6abbkxbdm3b1biw6gxnh6ca2sydvi3y5l2ys2")))) + "0l83r9idhrha1m21vpnw917m5dlldji49zvx4d25m5g3ia1pkhpf")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-edger" ,r-edger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gwascat" ,r-gwascat) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-universalmotif" ,r-universalmotif))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationhub + r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-deseq2 + r-dplyr + r-edger + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gwascat + r-iranges + r-magrittr + r-r-utils + r-readr + r-reshape2 + r-rlang + r-rtracklayer + r-s4vectors + r-seqinr + r-stringi + r-stringr + r-universalmotif)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/Aufiero/circRNAprofiler") (synopsis @@ -10349,21 +10725,21 @@ analysis, evolutionary conservation, biogenesis to functional analysis.") "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf")))) (build-system r-build-system) (propagated-inputs - `(("r-aucell" ,r-aucell) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-dosnow" ,r-dosnow) - ("r-dt" ,r-dt) - ("r-feather" ,r-feather) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-lda" ,r-lda) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-rcistarget" ,r-rcistarget) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-aucell + r-data-table + r-dplyr + r-dosnow + r-dt + r-feather + r-fitdistrplus + r-genomicranges + r-ggplot2 + r-lda + r-matrix + r-plyr + r-rcistarget + r-rtracklayer + r-s4vectors)) (home-page "https://github.com/aertslab/cisTopic") (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") (description @@ -10396,43 +10772,42 @@ cisTopics and explore the nature and regulatory proteins driving them.") "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2")))) (properties `((upstream-name . "cisTopic"))) (propagated-inputs - `(("r-aucell" ,r-aucell) - ("r-data-table" ,r-data-table) - ("r-dosnow" ,r-dosnow) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-feather" ,r-feather) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-lda" ,r-lda) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-rcistarget" ,r-rcistarget) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-text2vec" ,r-text2vec))) + (list r-aucell + r-data-table + r-dosnow + r-dplyr + r-dt + r-feather + r-fitdistrplus + r-genomicranges + r-ggplot2 + r-lda + r-matrix + r-plyr + r-rcistarget + r-rtracklayer + r-s4vectors + r-text2vec)) (native-inputs - `(("r-knitr" ,r-knitr)))))) + (list r-knitr))))) (define-public r-genie3 (package (name "r-genie3") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "1v54dzcz654wfm3npbp8gb55v49im0fm547cz3hvsidq4zhi3l1b")))) + "0ms769267pimrx3xwwkgjy03qilkxxs7xwhzfca01f65i4n3l6fw")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-reshape2" ,r-reshape2))) + (list r-dplyr r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GENIE3") (synopsis "Gene network inference with ensemble of trees") (description @@ -10443,18 +10818,18 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.68.1") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "1rmsrvn6hrg9ay7xfb05mfkxknnig78p3kbk9ghsd11lhx2fjm3s")))) + "1mgxpv5p6gnv04wzkcryrg5as5xrxvlqlkkcbv0k1bx9y6ykijy9")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) - (propagated-inputs - `(("r-knitr" ,r-knitr))) + (native-inputs + (list r-knitr)) (home-page "https://www.bioconductor.org/packages/ROC/") (synopsis "Utilities for ROC curves") (description @@ -10479,7 +10854,7 @@ Characteristic} (ROC) curves, with a focus on micro arrays.") `((upstream-name . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) (build-system r-build-system) - (propagated-inputs `(("r-minfi" ,r-minfi))) + (propagated-inputs (list r-minfi)) (home-page "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") (synopsis "Annotation for Illumina's 450k methylation arrays") @@ -10491,26 +10866,27 @@ data.") (define-public r-watermelon (package (name "r-watermelon") - (version "1.36.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "1qar8z0nf33bqr488swig0bfq8lnvcdjcxvw3q3b0hkkvybn27zw")))) + "1kzkg3cnm5pcs6blpw1qn7na6z3kar93v67680wsxa6qxxdiggk3")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-illuminahumanmethylation450kanno-ilmn12-hg19" - ,r-illuminahumanmethylation450kanno-ilmn12-hg19) - ("r-illuminaio" ,r-illuminaio) - ("r-limma" ,r-limma) - ("r-lumi" ,r-lumi) - ("r-matrixstats" ,r-matrixstats) - ("r-methylumi" ,r-methylumi) - ("r-roc" ,r-roc))) + (list r-biobase + r-illuminahumanmethylation450kanno-ilmn12-hg19 + r-illuminaio + r-limma + r-lumi + r-matrixstats + r-methylumi + r-roc)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/wateRmelon/") (synopsis "Illumina 450 methylation array normalization and metrics") (description @@ -10528,14 +10904,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "1w3z718q3bhh8bp71va9pbcd62pwbvgjw33ffg960jya40xssvc7")) + "147i33sb65n3cl3ibmjzgfm7i4ljy640k18mzknvc18v1906j9vp")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -10561,11 +10937,9 @@ metrics, with methods for objects produced by the @code{methylumi} and (properties `((upstream-name . "gdsfmt"))) (build-system r-build-system) (inputs - `(("lz4" ,lz4) - ("xz" ,xz) - ("zlib" ,zlib))) + (list lz4 xz zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://corearray.sourceforge.net/") (synopsis "R Interface to CoreArray Genomic Data Structure (GDS) Files") @@ -10586,24 +10960,27 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "061f0hc4m4nvdr6298pg3inpx1z2bpsm9nlxqs3v7n58q15xyzri")))) + "0ksbmybi8wsg515b4k9ij1xqqk9i90pyap2wq5w3c49qgc0pqali")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-gdsfmt" ,r-gdsfmt) - ("r-geoquery" ,r-geoquery) - ("r-methylumi" ,r-methylumi) - ("r-minfi" ,r-minfi) - ("r-watermelon" ,r-watermelon))) + (list r-biobase + r-biocgenerics + r-gdsfmt + r-geoquery + r-illuminaio + r-methylumi + r-minfi + r-watermelon)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/bigmelon/") (synopsis "Illumina methylation array analysis for large experiments") (description @@ -10614,20 +10991,18 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "06w43plv4x1pafybq633n7adqp9yj3bvaaamq7vylmkfbcx3nl8k")))) + "1q608c1madij8l52ljl3w52vi3cssr6ikny84yj6n8s7yvpx5jpr")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-rhtslib" ,r-rhtslib))) + (list r-biostrings r-genomicranges r-rhtslib)) (home-page "https://bioconductor.org/packages/seqbias/") (synopsis "Estimation of per-position bias in high-throughput sequencing data") (description @@ -10653,13 +11028,13 @@ genome sequence.") ;; doesn't make sense to build substitutes. (arguments `(#:substitutable? #f)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-bsgenome" ,r-bsgenome) - ("r-biostrings" ,r-biostrings))) + (list r-biocgenerics + r-s4vectors + r-iranges + r-genomeinfodb + r-genomicranges + r-bsgenome + r-biostrings)) (home-page "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") @@ -10678,20 +11053,18 @@ injected in that sequence).") (define-public r-reqon (package (name "r-reqon") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "1z13avbxwvvhh03arjfnaipznynifsi8k2hzw4kappz24f7lwmza")))) + "14v79vg3pmpkbzgn8xqd020jdwcs8g57d46bzl23yi3w1rsfbrb1")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs - `(("r-rjava" ,r-rjava) - ("r-rsamtools" ,r-rsamtools) - ("r-seqbias" ,r-seqbias))) + (list r-rjava r-rsamtools r-seqbias)) (home-page "https://bioconductor.org/packages/ReQON/") (synopsis "Recalibrating quality of nucleotides") (description @@ -10703,33 +11076,33 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "1sydzrqydfv1ik2h08xkxlx6xrv866bf0if6v5wch9l3krh0sych")))) + "1a1zhckrgq5yl51acj5piyh2hq70q6hhpym4cawzdssxhcbq70bk")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-foreach" ,r-foreach) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-mclust" ,r-mclust) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-foreach + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-hmisc + r-iranges + r-mclust + r-rsamtools + r-rtracklayer + r-s4vectors + r-seqinr + r-stringr)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/wavClusteR/") (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") (description @@ -10750,35 +11123,35 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "1095a2ynxcf9xiac5cjzslcbmjnjpbby0vy7d84qagdiq1w6mrhn")))) + "0fphnkkd3i7zf33a9lhw95n80vzv1z7fmn7mhrfb949yz4jdvk7d")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-edger" ,r-edger) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-proxy" ,r-proxy) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vegan" ,r-vegan) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-deseq2 + r-dplyr + r-dynamictreecut + r-edger + r-ggplot2 + r-hmisc + r-limma + r-magrittr + r-proxy + r-s4vectors + r-summarizedexperiment + r-tibble + r-tidyr + r-vegan + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") (synopsis "Analysis for short time-series data") (description @@ -10791,42 +11164,42 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "0abhrk53csd9jz9sv4q1qr74jax9mbj2icbz1iilf1123nvnjypd")))) + "15js8xzi9rsgkjkqcshzk3r3g85kdnxn5v2hi6l5s4yxj9lnq12p")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dt" ,r-dt) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicscores" ,r-genomicscores) - ("r-graph" ,r-graph) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-rbgl" ,r-rbgl) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs) - ("r-shinythemes" ,r-shinythemes) - ("r-shinytree" ,r-shinytree) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation) - ("r-xvector" ,r-xvector))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-dt + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-genomicscores + r-graph + r-gviz + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-shiny + r-shinyjs + r-shinythemes + r-shinytree + r-summarizedexperiment + r-variantannotation + r-xvector)) (home-page "https://github.com/rcastelo/VariantFiltering") (synopsis "Filtering of coding and non-coding genetic variants") (description @@ -10849,7 +11222,7 @@ populations, splice site strength, conservation, etc.") (properties `((upstream-name . "GenomeGraphs"))) (build-system r-build-system) (propagated-inputs - `(("r-biomart" ,r-biomart))) + (list r-biomart)) (home-page "https://bioconductor.org/packages/GenomeGraphs/") (synopsis "Plotting genomic information from Ensembl") (description @@ -10877,16 +11250,16 @@ same genome coordinate system.") (properties `((upstream-name . "waveTiling"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-genomegraphs" ,r-genomegraphs) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-oligo" ,r-oligo) - ("r-oligoclasses" ,r-oligoclasses) - ("r-preprocesscore" ,r-preprocesscore) - ("r-waveslim" ,r-waveslim))) + (list r-affy + r-biobase + r-biostrings + r-genomegraphs + r-genomicranges + r-iranges + r-oligo + r-oligoclasses + r-preprocesscore + r-waveslim)) (home-page "https://r-forge.r-project.org/projects/wavetiling/") (synopsis "Wavelet-based models for tiling array transcriptome analysis") (description @@ -10897,36 +11270,37 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "1pqy2g9pg8pswmkrs2fzlkwwliw2r7f33h05bci5bz41b8ribpzj")))) + "0f5y61dpzwmr8v7npim18zvxa8n49rbzclb9j72haba0px6ibhvw")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocparallel" ,r-biocparallel) - ("r-colorramps" ,r-colorramps) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-gplots" ,r-gplots) - ("r-iterators" ,r-iterators) - ("r-limma" ,r-limma) - ("r-lme4" ,r-lme4) - ("r-lmertest" ,r-lmertest) - ("r-mass" ,r-mass) - ("r-pbkrtest" ,r-pbkrtest) - ("r-progress" ,r-progress) - ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocparallel + r-doparallel + r-foreach + r-ggplot2 + r-gplots + r-iterators + r-limma + r-lme4 + r-lmertest + r-mass + r-matrix + r-pbkrtest + r-progress + r-reshape2 + r-rlang + r-scales)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/variancePartition/") (synopsis "Analyze variation in gene expression experiments") (description @@ -10941,22 +11315,18 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "1y3ik5a9w66jby6682jfm8mn2883s8yfv4xw8a8v1f6q2d1j938l")))) + "1d7qj5yv6kzqmdrnp5pd8qv1yr4bg8cs39p8ib0i0k8b4wr97kq3")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-gplots" ,r-gplots) - ("r-limma" ,r-limma) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer)) (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" "groups/bertone/software/HTqPCR.pdf")) (synopsis "Automated analysis of high-throughput qPCR data") @@ -10975,20 +11345,19 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1clcz610sl3s0mjf84j21xgrmjhkxcc4h292ljwq5yzbkk68g896")))) + "0kw26bm2yyna38q5r4zb2alpa3j4gx7v970419mnjlif4g0hmggk")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-htqpcr" ,r-htqpcr))) + (list r-biocgenerics r-htqpcr)) (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") (description @@ -11000,14 +11369,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.10.2") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "0hv2v2zgif5ihr5hxmdz32rln43jc1j0rslp44kd3rijjl45zysn")))) + "1p9zdrsxqn4ayvbj05xgpzpbzkzrh7k0d62x10069687vfl6dlxg")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -11019,18 +11388,18 @@ data.") (substitute* "src/Makevars" (("/usr/bin/strip") (which "strip")))))))) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-rcppthread" ,r-rcppthread) - ("r-rlang" ,r-rlang) - ("r-s4vectors" ,r-s4vectors) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-ggplot2 + r-iranges + r-mass + r-rcpp + r-rcppthread + r-rlang + r-s4vectors + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/universalmotif/") (synopsis @@ -11050,27 +11419,30 @@ motifs, and others.") (define-public r-activedriverwgs (package (name "r-activedriverwgs") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "ActiveDriverWGS" version)) (sha256 (base32 - "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say")))) + "13b5yazgv9kckcp6gck183mh1m0q8lc5ixagmcy9s8kv2wz7wq45")))) (properties `((upstream-name . "ActiveDriverWGS"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-bsgenome-hsapiens-ucsc-hg38 + r-bsgenome-mmusculus-ucsc-mm9 + r-bsgenome-mmusculus-ucsc-mm10 + r-genomeinfodb + r-genomicranges + r-iranges + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") (synopsis "Driver discovery tool for cancer whole genomes") (description @@ -11085,22 +11457,21 @@ using whole genome sequencing data.") (define-public r-activepathways (package (name "r-activepathways") - (version "1.0.2") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "ActivePathways" version)) (sha256 (base32 - "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l")))) + "1prhwx0nnwy2q62l2r0z31mhk4mq6xdr6mjihdlwpwgwq4rfi60y")))) (properties `((upstream-name . "ActivePathways"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2))) + (list r-data-table r-ggplot2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActivePathways/") (synopsis "Multivariate pathway enrichment analysis") (description @@ -11114,18 +11485,18 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "1gp40ddspblpszzm4k4r7ysgx883iwdfqc5ds23p2q1ml9idwgvv")))) + "0x1sx319yfxgkscr9r62msq00ddvmzryzn42wy4dh5pvjmgifkkn")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs - `(("r-kernsmooth" ,r-kernsmooth))) + (list r-kernsmooth)) (home-page "https://bioconductor.org/packages/BGmix/") (synopsis "Bayesian models for differential gene expression") (description @@ -11136,21 +11507,18 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "18n6j2ihv85rhai5sf5k3mwf9nkc2nl2sinx3rrs6sbl529g4mw4")))) + "0z3isnpyf9s11807dprxmd105lb0k4l7r1sygad30ncjvpldifzm")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-gcrma" ,r-gcrma) - ("r-rcpp" ,r-rcpp))) + (list r-affy r-biobase r-gcrma r-rcpp)) (home-page "https://bioconductor.org/packages/bgx/") (synopsis "Bayesian gene expression") (description @@ -11161,14 +11529,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "0aaawm7h3ppyyhd7hi14rpynagnxx4730f5vxizj5bpzwbclp6h9")))) + "09nw4ljc9sn7iw09ha0m614hmdjj193xhhav5x5p07l501kks6h2")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") @@ -11187,20 +11555,18 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "0j3gs4xcdgaca2c62jf2h86skbbxm1c9g2khs5bsa8fmkskr6vl9")))) + "1g8vrsc05cysb36gsw8sfmr6dgbh4aji37vcq9qwkmkv3jgvnlf6")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-gseabase" ,r-gseabase) - ("r-multtest" ,r-multtest))) + (list r-biobase r-gseabase r-multtest)) (home-page "http://bioinfo.curie.fr") (synopsis "Biclustering analysis and results exploration") (description @@ -11211,21 +11577,20 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "1fwy7ws0bn67557s0kcw8pbln2jg834n6kfbs8297ps07nxr0lpj")))) + "0vidypvphnj76g4ra5ijrgqx2dnzw0fmvdvz35gsqswrr3k20jkk")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-poibin" ,r-poibin))) + (list r-genomicranges r-poibin)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiFET") (synopsis "Bias-free footprint enrichment test") (description @@ -11241,23 +11606,22 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "017xwra6ms7kx6sg3ksw1vr9zn23imc2qjgpmjikx7mgbak125xh")))) + "0mdyr637sgasc156cv8i2s2mpl1hdvilfwwkhvw7l95pl90gnsh2")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs - `(("libsbml" ,libsbml))) + (list libsbml)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-graph" ,r-graph))) + (list r-biocgenerics r-graph)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://www.sbml.org") (synopsis "R support for SBML") (description @@ -11268,18 +11632,18 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "01knpd964m2g9vwd7c72qnc8g2p2pzhvk7lin4mhvcmb3pvsdlh7")))) + "0xnyl9qh5p32ifvzkcl5g4a38zbnwykqzrp8gwz076a0ksiqqdxf")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph))) + (list r-graph)) (home-page "https://bioconductor.org/packages/hypergraph") (synopsis "Hypergraph data structures") (description @@ -11290,21 +11654,19 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "1qkxixkgvvfha0ii8rwwcbrbjmbbxsy8afv5ymcq01k3hbykx44r")))) + "1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) - (inputs `(("graphviz" ,graphviz))) + (inputs (list graphviz)) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-hypergraph" ,r-hypergraph) - ("r-rgraphviz" ,r-rgraphviz))) + (list r-graph r-hypergraph r-rgraphviz)) (home-page "https://bioconductor.org/packages/hyperdraw") (synopsis "Visualizing hypergraphs") (description @@ -11314,23 +11676,23 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "1y9659pxm65w51zvrz36girb3qvfc64zijjkxmg6xn4pbc8vv1wf")))) + "1g01666wwznk148776s4vr1hfi3dfl448dhgk4d1qy2wv6sxh9kr")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs - `(("r-hyperdraw" ,r-hyperdraw) - ("r-hypergraph" ,r-hypergraph) - ("r-lim" ,r-lim) - ("r-limsolve" ,r-limsolve) - ("r-rsbml" ,r-rsbml) - ("r-stringr" ,r-stringr))) + (list r-hyperdraw + r-hypergraph + r-lim + r-limsolve + r-rsbml + r-stringr)) (home-page "https://bioconductor.org/packages/BiGGR/") (synopsis "Constraint based modeling using metabolic reconstruction databases") (description @@ -11356,9 +11718,9 @@ networks and estimated fluxes can be visualized with hypergraphs.") `((upstream-name . "bigmemoryExtras"))) (build-system r-build-system) (propagated-inputs - `(("r-bigmemory" ,r-bigmemory))) + (list r-bigmemory)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/phaverty/bigmemoryExtras") (synopsis "Extension of the bigmemory package") (description @@ -11378,37 +11740,37 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "0yrg9x1a92zmz7j5hk77cph1jg82mkpr7k7qi9fdr6z5nqq6fgz6")))) + "0b0l0v9p7a5da3x18d0pqn41ilgxfyzapjaawgsshcfm5mjq5d7q")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-dplyr" ,r-dplyr) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-hexbin" ,r-hexbin) - ("r-hmisc" ,r-hmisc) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-plotly" ,r-plotly) - ("r-plyr" ,r-plyr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape" ,r-reshape) - ("r-shiny" ,r-shiny) - ("r-shinycssloaders" ,r-shinycssloaders) - ("r-shinydashboard" ,r-shinydashboard) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-delayedarray + r-dplyr + r-ggally + r-ggplot2 + r-gridextra + r-hexbin + r-hmisc + r-htmlwidgets + r-plotly + r-plyr + r-rcolorbrewer + r-reshape + r-shiny + r-shinycssloaders + r-shinydashboard + r-stringr + r-summarizedexperiment + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/lindsayrutter/bigPint") (synopsis "Big multivariate data plotted interactively") (description @@ -11421,32 +11783,34 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.44.0") + (version "3.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1z59npqk7hnqzhjdnry6lfqlyxfzwqprp7bmbdzs4rp22pzcv1v8")))) + "069xd7if7fs69afmamgl6wrkzpnk97ic6z5ix4vvlzkb078dm0p8")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-bh" ,r-bh) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-digest" ,r-digest) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-png" ,r-png) - ("r-rcpp" ,r-rcpp) - ("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson) - ("r-rsvg" ,r-rsvg))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-base64enc + r-bh + r-biocgenerics + r-dbi + r-digest + r-dt + r-ggplot2 + r-gridextra + r-jsonlite + r-png + r-rcpp + r-rcurl + r-rjson + r-rsvg + r-stringi)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/girke-lab/ChemmineR") (synopsis "Cheminformatics toolkit for R") (description @@ -11459,29 +11823,58 @@ visualization functions for compound clustering results and chemical structures.") (license license:artistic2.0))) +(define-public r-fmcsr + (package + (name "r-fmcsr") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "fmcsR" version)) + (sha256 + (base32 "0mshslfj7jsix1yc03s54spbbi56zspic49kfsjfv8npikj1i5w0")))) + (properties `((upstream-name . "fmcsR"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics r-chemminer r-runit)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/girke-lab/fmcsR") + (synopsis "Mismatch tolerant maximum common substructure searching") + (description + "The fmcsR package introduces an efficient @dfn{maximum common +substructure} (MCS) algorithms combined with a novel matching strategy that +allows for atom and/or bond mismatches in the substructures shared among two +small molecules. The resulting flexible MCSs (FMCSs) are often larger than +strict MCSs, resulting in the identification of more common features in their +source structures, as well as a higher sensitivity in finding compounds with +weak structural similarities. The fmcsR package provides several utilities to +use the FMCS algorithm for pairwise compound comparisons, structure similarity +searching and clustering.") + (license license:artistic2.0))) + (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.30.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "1mlv80w8a7l8cii3dfqvanvh0qdqvcg8c1iiq4xlyvkjxfs64ka1")))) + "0pa8d7p9asp36wddkg779i3b9m12rxik56c54bmclnammr0cz89i")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-chemminer" ,r-chemminer) - ("r-dbi" ,r-dbi) - ("r-matrix" ,r-matrix) - ("r-rjson" ,r-rjson) - ("r-rsqlite" ,r-rsqlite) - ("r-xml" ,r-xml))) + (list r-biocgenerics + r-chemminer + r-dbi + r-matrix + r-rjson + r-rsqlite + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/girke-lab/bioassayR") (synopsis "Cross-target analysis of small molecule bioactivity") (description @@ -11497,23 +11890,20 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "1ybyhmrcvj6k1laxw9bc8jbn533frkzh9k8kl1ibd5pi368rfqzn")))) + "034gbywrscv23kk1qnk7sc7dxdckmf60wh29fz65v1n28mkf180r")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-tidyr" ,r-tidyr))) + (list r-biobase r-broom r-dplyr r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/StoreyLab/biobroom") (synopsis "Turn Bioconductor objects into tidy data frames") (description @@ -11529,24 +11919,18 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "11bgz6951nfygxp3fm0190gf2bb5zplis1bc0am4757liw4qybhf")))) + "0wmdv4j6dinszxwpz2jddshkh1ahbhm2fxh6vhjsk4grw38i1lfr")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-checkmate" ,r-checkmate) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-rappdirs" ,r-rappdirs))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi r-checkmate r-graph r-httr r-rappdirs)) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description @@ -11558,27 +11942,27 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1293z89ai766c559axgr7mz5x4564gyl9xqzf6s8s0aj1xb35gqf")))) + "1f4kd5cql7knnqaq3ba48kkypw8p60lkfdsnpqxcabdj30gqp55b")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dose" ,r-dose) - ("r-enrichplot" ,r-enrichplot) - ("r-ggplot2" ,r-ggplot2) - ("r-ggraph" ,r-ggraph) - ("r-graphite" ,r-graphite) - ("r-igraph" ,r-igraph) - ("r-reactome-db" ,r-reactome-db))) + (list r-annotationdbi + r-dose + r-enrichplot + r-ggplot2 + r-ggraph + r-graphite + r-igraph + r-reactome-db)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/ReactomePA") (synopsis "Reactome pathway analysis") (description @@ -11590,20 +11974,18 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "1k1kl0m7wzaqpv7i20pfav2a6jf93bhri4w7qdikmvkf011n9422")))) + "10dw6c93rmpknzf4cnhw3y7lb27q4xq7x7wirl2a7qywdj0yj2g6")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-cluster" ,r-cluster) - ("r-lattice" ,r-lattice))) + (list r-biobase r-cluster r-lattice)) (home-page "https://bioconductor.org/packages/EBarrays/") (synopsis "Gene clustering and differential expression identification") (description @@ -11625,7 +12007,7 @@ microarray data.") (properties `((upstream-name . "BiocCaseStudies"))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/BiocCaseStudies") (synopsis "Support for the case studies monograph") (description @@ -11636,27 +12018,27 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1h0l5w33c9jpc20pynq634qmx8jbfa802d7jslmf4haljmrxm4a1")))) + "0w9ddicyp9i8rxf92n9pghd9s6bb8jdjikaylrmkydhb7jbhan0y")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-knitr" ,r-knitr) - ("r-optparse" ,r-optparse) - ("r-biocmanager" ,r-biocmanager) - ("r-biocviews" ,r-biocviews) - ("r-stringdist" ,r-stringdist))) + (list r-codetools + r-graph + r-httr + r-knitr + r-optparse + r-biocmanager + r-biocviews + r-stringdist)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocCheck") (synopsis "Executes Bioconductor-specific package checks") (description "This package contains tools to perform additional quality @@ -11666,21 +12048,18 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "12bmj9kdlylp02cfwviak7y323ndccl2694rvi4cdg4vsx7v3ya3")))) + "0c7r0c1kx22dlwi6d1ldbkkbf53yi0p3vmgbwzrbkn3cina7bcxq")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-geneplotter" ,r-geneplotter) - ("r-graph" ,r-graph) - ("r-rgraphviz" ,r-rgraphviz))) + (list r-biocgenerics r-geneplotter r-graph r-rgraphviz)) (home-page "https://bioconductor.org/packages/biocGraph/") (synopsis "Graph examples and use cases in Bioinformatics") (description @@ -11691,24 +12070,20 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.20.2") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "0p2wdq5vrx63ndghl9ww428z2lwnv5y88xmcr51by2g6vcj3brcf")))) + "0xx6xr01sb5wig94515zxgw24r9fv0g962ajy87741civhq32lbd")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) - ("r-bookdown" ,r-bookdown) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-yaml" ,r-yaml))) + (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocStyle") (synopsis "Bioconductor formatting styles") (description "This package provides standard formatting styles for @@ -11719,24 +12094,24 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.60.0") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0pc5ll59vm8a9s1nrdc7p9wk11a52rrz669fsrrqd8qapa8p6wfd")))) + "1v6himzp546dpb990vv0nlya21w8x2x30137rsmahjzg942nzs9r")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-graph" ,r-graph) - ("r-rbgl" ,r-rbgl) - ("r-rcurl" ,r-rcurl) - ("r-xml" ,r-xml) - ("r-runit" ,r-runit))) + (list r-biobase + r-biocmanager + r-graph + r-rbgl + r-rcurl + r-xml + r-runit)) (home-page "https://bioconductor.org/packages/biocViews") (synopsis "Bioconductor package categorization helper") (description "The purpose of biocViews is to create HTML pages that @@ -11747,26 +12122,26 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "1mzmw3100lf33yhz27nbxncrjk5bprlackrjcwf8xdhcaidg40p4")))) + "15las4qmqvrn81hczxa3ylikqh54kp1lg9r8rcyfvrx5l0kgwlfq")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-curl" ,r-curl) - ("r-rappdirs" ,r-rappdirs) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationhub + r-biocfilecache + r-biocgenerics + r-biocmanager + r-curl + r-rappdirs + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ExperimentHub/") (synopsis "Client to access ExperimentHub resources") (description @@ -11781,24 +12156,24 @@ access.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "1h63vg1iskw79ijg5h1b9097ams8pp3kvnlawlfci6xfli07xpkj")))) + "1jcj29df4prknqwbydca1jb9w6njacjhwwk9jp0r5mvb88xrm60s")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs - `(("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-mass" ,r-mass) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-mass + r-rtracklayer + r-s4vectors)) (home-page "https://github.com/Kraus-Lab/groHMM") (synopsis "GRO-seq analysis pipeline") (description @@ -11808,27 +12183,27 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "0l0arf3q1f6zy6pdgsy3h5n523sg1hlilv7lj7snr5814idgdj51")))) + "1h3b8vqlbd04amjprxd1814zksdrbi01a0xn3906vkbqi43hfyn9")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr))) + (list r-biobase + r-biocgenerics + r-genomicranges + r-iranges + r-s4vectors + r-summarizedexperiment + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://waldronlab.io/MultiAssayExperiment/") (synopsis "Integration of multi-omics experiments in Bioconductor") (description @@ -11843,41 +12218,41 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1ix09a39z7y2cj0y8qsd66ka8a8y8q79w08l4jv1yhhn9h4va89s")))) + "1h5s6wbc5n5x5d28rynxpcmaklxdhf72g9gg9fy8cg77niipvxd9")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs - `(("r-bigrquery" ,r-bigrquery) - ("r-car" ,r-car) - ("r-complexheatmap" ,r-complexheatmap) - ("r-curatedtcgadata" ,r-curatedtcgadata) - ("r-dbi" ,r-dbi) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rjson" ,r-rjson) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-bigrquery + r-car + r-complexheatmap + r-curatedtcgadata + r-dbi + r-dplyr + r-dt + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggpubr + r-graph + r-httr + r-iranges + r-magrittr + r-plyr + r-rgraphviz + r-rjson + r-s4vectors + r-scales + r-shiny + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocOncoTK") (synopsis "Bioconductor components for general cancer genomics") (description @@ -11888,22 +12263,20 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "135rga7mwpzy8ypvriqpbmlh9l5yf61s9s1sa9615qfab14jh06b")))) + "0ii4g7438lb34ykidkbxw3v3k289k662rgbgayf9gak5avpkb2cq")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-gseabase" ,r-gseabase) - ("r-matrix" ,r-matrix))) + (list r-biocparallel r-gseabase r-matrix)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://llrs.github.io/BioCor/") (synopsis "Functional similarities") (description @@ -11917,41 +12290,41 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.10.2") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "1sfp1nxlwbbbpx2iwvyk9p10jdy2vxhgn2b5fy5blayzjjlb3d80")))) + "1yz2sgx4xrnw22k3d6q6hkj213bnbb4hbr5ymxnmjnsz551s75ny")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biocfilecache" ,r-biocfilecache) - ("r-biocmanager" ,r-biocmanager) - ("r-biocviews" ,r-biocviews) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-gh" ,r-gh) - ("r-graph" ,r-graph) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-httr" ,r-httr) - ("r-igraph" ,r-igraph) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-rbgl" ,r-rbgl) - ("r-readr" ,r-readr) - ("r-rlang" ,r-rlang) - ("r-rvest" ,r-rvest) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocfilecache + r-biocmanager + r-biocviews + r-dplyr + r-dt + r-gh + r-graph + r-htmltools + r-htmlwidgets + r-httr + r-igraph + r-jsonlite + r-magrittr + r-rbgl + r-readr + r-rlang + r-rvest + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-xml2)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/seandavi/BiocPkgTools") (synopsis "Collection of tools for learning about Bioconductor packages") (description @@ -11965,29 +12338,29 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.6.1") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "0nmrg9cgq8l9w467y364jghnvym05abpj8pyj90grmrib2xc5sj2")))) + "1x5ar9byr85iap2x6y66j31fi17wr31awx1gl3z01sckp0dldx6w")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocio" ,r-biocio) - ("r-dplyr" ,r-dplyr) - ("r-keggrest" ,r-keggrest) - ("r-ontologyindex" ,r-ontologyindex) - ("r-plyr" ,r-plyr) - ("r-rlang" ,r-rlang) - ("r-s4vectors" ,r-s4vectors) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-annotationdbi + r-biocio + r-dplyr + r-keggrest + r-ontologyindex + r-plyr + r-rlang + r-s4vectors + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocSet") (synopsis @@ -12003,29 +12376,29 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "1a32bwgnxaw0gv2gij2p4rm0a6l06jjhidvfz2v4k900pz1w79av")))) + "1j9s8w5y8savcmh70npkanxacq1kipxnwk1wsiw5hwnp1p13ldaa")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biocstyle" ,r-biocstyle) - ("r-bookdown" ,r-bookdown) - ("r-git2r" ,r-git2r) - ("r-httr" ,r-httr) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rstudioapi" ,r-rstudioapi) - ("r-stringr" ,r-stringr) - ("r-usethis" ,r-usethis))) + (list r-biocstyle + r-bookdown + r-git2r + r-httr + r-knitr + r-rmarkdown + r-rstudioapi + r-stringr + r-usethis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") (synopsis "Tools to aid the development of Bioconductor Workflow packages") (description @@ -12036,19 +12409,18 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "1y1x9q9aa76gbhsyfn638rxp5icjvq30fv3a4205xh7g5jwlf6yw")))) + "0y35c9sdq5x4q64ip0wgqz59mh01l71k1pp6n8vqbr667nwg0gdp")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-kernsmooth" ,r-kernsmooth))) + (list r-biobase r-kernsmooth)) (home-page "https://bioconductor.org/packages/bioDist/") (synopsis "Different distance measures") (description @@ -12059,32 +12431,32 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "11idi9fwvyhkakbm63qxcdhkany8gbskis04z0p5a39lppq8ks31")))) + "10kfhsxhsjpzal3yvcqg769h5fz99cqqjq217cj9jip3jfh2m2h4")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-bh" ,r-bh) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-cowplot" ,r-cowplot) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dqrng" ,r-dqrng) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-lattice" ,r-lattice) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-bh + r-biocparallel + r-biocsingular + r-cowplot + r-delayedarray + r-delayedmatrixstats + r-dqrng + r-ggplot2 + r-ggrepel + r-lattice + r-matrix + r-rcpp + r-reshape2)) + (native-inputs (list r-knitr)) (home-page "https://github.com/kevinblighe/PCAtools") (synopsis "PCAtools: everything Principal Components Analysis") (description @@ -12105,23 +12477,19 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0ads9c9i8b39wvjih057zlyivj8zpsqjxf6r97yflz4sbi1jmcji")))) + "0kr61mhxp9phn1136fci450zwfhsipchmlm8d5rgib4lh0zbxrhl")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-getoptlong" ,r-getoptlong) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson)) + (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/rGREAT") (synopsis "Client for GREAT analysis") (description @@ -12133,28 +12501,28 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "17gj4haa4ywc6bmppm342jzppl3inqa94235yspikij6c098vrmc")))) + "0jsql5wd58hs5mnn9wq5b4kl3z57y6amykirfb3k047zpyi8ijnh")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-corpcor" ,r-corpcor) - ("r-doparallel" ,r-doparallel) - ("r-dosnow" ,r-dosnow) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-matrix" ,r-matrix) - ("r-matrixcalc" ,r-matrixcalc) - ("r-rtsne" ,r-rtsne) - ("r-umap" ,r-umap))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-cluster + r-corpcor + r-doparallel + r-dosnow + r-foreach + r-ggplot2 + r-matrix + r-matrixcalc + r-rtsne + r-umap)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/M3C") (synopsis "Monte Carlo reference-based consensus clustering") (description @@ -12166,18 +12534,18 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "1rzgwxx4w2bqsaz0xmkhi4w9zsxgms80xf59zg1xp1camyhaihlz")))) + "08jd7g28mazvwd3qbq8y26czmkz45avp4vy8l7i5d6qajwzqzgzs")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival))) + (list r-survival)) (home-page "https://bioconductor.org/packages/Icens") (synopsis "NPMLE for censored and truncated data") (description @@ -12191,21 +12559,18 @@ truncated data.") (define-public r-interval (package (name "r-interval") - (version "1.1-0.7") + (version "1.1-0.8") (source (origin (method url-fetch) (uri (cran-uri "interval" version)) (sha256 (base32 - "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9")))) + "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl")))) (properties `((upstream-name . "interval"))) (build-system r-build-system) (propagated-inputs - `(("r-icens" ,r-icens) - ("r-mlecens" ,r-mlecens) - ("r-perm" ,r-perm) - ("r-survival" ,r-survival))) + (list r-icens r-mlecens r-perm r-survival)) (home-page "https://cran.r-project.org/web/packages/interval/") (synopsis "Weighted Logrank tests and NPMLE for interval censored data") (description @@ -12229,11 +12594,7 @@ plot them, and perform logrank or Wilcoxon type tests.") (properties `((upstream-name . "FHtest"))) (build-system r-build-system) (propagated-inputs - `(("r-interval" ,r-interval) - ("r-kmsurv" ,r-kmsurv) - ("r-mass" ,r-mass) - ("r-perm" ,r-perm) - ("r-survival" ,r-survival))) + (list r-interval r-kmsurv r-mass r-perm r-survival)) (home-page "https://cran.r-project.org/web/packages/FHtest/") (synopsis "Tests for survival data based on the Fleming-Harrington class") (description @@ -12262,23 +12623,23 @@ with: (properties `((upstream-name . "FourCSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-deseq2" ,r-deseq2) - ("r-fda" ,r-fda) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-gtools" ,r-gtools) - ("r-lsd" ,r-lsd) - ("r-matrix" ,r-matrix) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biostrings + r-deseq2 + r-fda + r-genomicalignments + r-genomicranges + r-ggbio + r-ggplot2 + r-gtools + r-lsd + r-matrix + r-reshape2 + r-rsamtools + r-rtracklayer + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") (synopsis "Analysis of multiplexed 4C sequencing data") @@ -12296,14 +12657,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "17a00blz4kvhmsk92bp5alj9kdpy7h1id7nk4vqxakhkb2jabr20")))) + "1i93vdqa6pwzamiryp3lv6cyvhx9shs01is0q6vbmdvcbii2vf3x")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -12317,18 +12678,18 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.30.1") + (version "0.32.3") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "103sw0fmmm4f3hprrsn7dwg0kmmr9mcmb46dcwwb6p5np0al2sfx")))) + "0wp29v41f9cf6khq2ww0f63nsq6219l1ycajzdqp3a2xda734ncw")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) + (list r-biocgenerics)) (home-page "https://bioconductor.org/packages/S4Vectors") (synopsis "S4 implementation of vectors and lists") (description @@ -12357,18 +12718,18 @@ S4Vectors package itself.") (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-doparallel" ,r-doparallel) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-fastcluster" ,r-fastcluster) - ("r-foreach" ,r-foreach) - ("r-go-db" ,r-go-db) - ("r-hmisc" ,r-hmisc) - ("r-impute" ,r-impute) - ("r-rcpp" ,r-rcpp) - ("r-survival" ,r-survival) - ("r-matrixstats" ,r-matrixstats) - ("r-preprocesscore" ,r-preprocesscore))) + (list r-annotationdbi + r-doparallel + r-dynamictreecut + r-fastcluster + r-foreach + r-go-db + r-hmisc + r-impute + r-rcpp + r-survival + r-matrixstats + r-preprocesscore)) (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") (synopsis "Weighted correlation network analysis") @@ -12384,14 +12745,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "0d0xq1vgr4b165cn4wg7zmfjyc1d9ir4amgs196j4cgrhpmrnl8s")))) + "0fyv1ybpahkwz3fawzxgxfnshi8y7c18262rgdmqwdl5662vv1p7")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments @@ -12407,11 +12768,11 @@ data manipulation and visualization.") ;; FIXME: Rgraphviz bundles the sources of an older variant of ;; graphviz. It does not build with the latest version of graphviz, so ;; we do not add graphviz to the inputs. - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-graph" ,r-graph))) + (list r-graph)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://bioconductor.org/packages/Rgraphviz") (synopsis "Plotting capabilities for R graph objects") (description @@ -12422,21 +12783,19 @@ objects from the @code{graph} package.") (define-public r-fithic (package (name "r-fithic") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1p8a6lis5yswaj647bjw89harlarnsxmvjzz63fn1l6gxrwhh8bx")))) + "0a3d2bxp98lmbf3i864zgfwxwvxyqfcrh75z9yz7ra7y44pkjr4y")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-fdrtool" ,r-fdrtool) - ("r-rcpp" ,r-rcpp))) + (list r-data-table r-fdrtool r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/FitHiC") (synopsis "Confidence estimation for intra-chromosomal contact maps") (description @@ -12448,23 +12807,23 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0s3kfqs3zlmq61hxdmxpmi9gfs9w3byckw7xzp1hrhdbsl46yvgq")))) + "1ckiwqfq86k8p3y36iwr7k3y6g4z80n8hb047c0i2491lrn23rhx")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer))) + (list r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-rcolorbrewer + r-rtracklayer)) (home-page "https://bioconductor.org/packages/HiTC") (synopsis "High throughput chromosome conformation capture analysis") (description @@ -12477,27 +12836,27 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.20.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1718hplz5qlbwxwb87509bl7lir9kilvn1s7p2haz551pg48zvrc")))) + "1al4a88pgdl7hfhphsnwl1gg1c1kmw37wcdr4v4pfsw5l8ff7nx4")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rhdf5" ,r-rhdf5) - ("r-rhdf5filters" ,r-rhdf5filters) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-s4vectors" ,r-s4vectors))) + (list zlib)) + (propagated-inputs + (list r-biocgenerics + r-delayedarray + r-iranges + r-matrix + r-rhdf5 + r-rhdf5filters + r-rhdf5lib + r-s4vectors)) (home-page "https://bioconductor.org/packages/HDF5Array") (synopsis "HDF5 back end for DelayedArray objects") (description "This package provides an array-like container for convenient @@ -12508,14 +12867,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1cwynbcaaxmbh45fc0d264liqdj0wbjlj7k2bsq3qfjbnh6kkam5")) + "0yly9s3wdnhd9ci2jxfkql38ibv35yzs38a6g6ashbg1m5kgwd9p")) (modules '((guix build utils))) (snippet '(begin @@ -12577,8 +12936,7 @@ block processing.") (("cp \"\\$\\{SZIP_LIB\\}.*") "") (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))))))) (propagated-inputs - `(("hdf5" ,hdf5-1.10) - ("zlib" ,zlib))) + (list hdf5-1.10 zlib)) (native-inputs `(("hdf5-source" ,(package-source hdf5-1.10)) ("r-knitr" ,r-knitr))) @@ -12591,22 +12949,19 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.8.1") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "06bpfpddsl49csxrs8hlx5pv0absc2wdcparchf8qqaqydazwci2")))) + "1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-biocgenerics r-delayedarray r-matrix r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/beachmat") (synopsis "Compiling Bioconductor to handle each matrix type") (description "This package provides a consistent C++ class interface for a @@ -12620,38 +12975,38 @@ matrices.") (define-public r-cner (package (name "r-cner") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "13w0gsfm7k29dp5nb0c9sb2ix506ph6dixsjis6xxcz6acq7lg2k")))) + (base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-go-db" ,r-go-db) - ("r-iranges" ,r-iranges) - ("r-keggrest" ,r-keggrest) - ("r-powerlaw" ,r-powerlaw) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (inputs (list zlib)) + (propagated-inputs + (list r-annotate + r-biocgenerics + r-biostrings + r-dbi + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-go-db + r-iranges + r-keggrest + r-powerlaw + r-r-utils + r-readr + r-reshape2 + r-rsqlite + r-rtracklayer + r-s4vectors + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/ge11232002/CNEr") (synopsis "CNE Detection and Visualization") (description @@ -12668,38 +13023,38 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "1avgjv2nyr28cla0z9dvh3v0hr1f561sz2as1k53a42irbjk0var")))) + "0j5gv145fczzdspwhbywlg47y05pgnkra9jg7bn4wa1k0cf5pr9g")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-catools" ,r-catools) - ("r-cner" ,r-cner) - ("r-dbi" ,r-dbi) - ("r-dirichletmultinomial" ,r-dirichletmultinomial) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqlogo" ,r-seqlogo) - ("r-tfmpvalue" ,r-tfmpvalue) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-catools + r-cner + r-dbi + r-dirichletmultinomial + r-genomeinfodb + r-genomicranges + r-gtools + r-iranges + r-rsqlite + r-rtracklayer + r-s4vectors + r-seqlogo + r-tfmpvalue + r-xml + r-xvector)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ge11232002/TFBSTools") (synopsis "Transcription factor binding site (TFBS) analysis") (description @@ -12711,33 +13066,57 @@ scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.") (license license:gpl2))) +(define-public r-maftools + (package + (name "r-maftools") + (version "2.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "maftools" version)) + (sha256 + (base32 "1s8w3xwwigz803l81bs9cb2dbvvw5r9z8jjcav1rmh9wm8909nfd")))) + (properties `((upstream-name . "maftools"))) + (build-system r-build-system) + (propagated-inputs + (list r-data-table r-rcolorbrewer r-rhtslib r-survival r-zlibbioc)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/PoisonAlien/maftools") + (synopsis "Summarize, analyze and visualize MAF files") + (description + "Analyze and visualize Mutation Annotation Format (MAF) files from large +scale sequencing studies. This package provides various functions to perform +most commonly used analyses in cancer genomics and to create feature rich +customizable visualzations with minimal effort.") + (license license:expat))) + (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "1vif3dp4lv4jz1pxsq0ig791ir8q65jmrlqmkyfxpfxfj5alqnbm")))) + "0f7j54zdn51h1gcn81vqs8avmschjwqprjcfpvsi00q4fna3fg7z")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tfbstools" ,r-tfbstools))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-rcpp + r-rcpparmadillo + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-tfbstools)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/motifmatchr") (synopsis "Fast motif matching in R") (description @@ -12748,39 +13127,39 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "1birmwvcvl2hb5ygbsb3wvbdfayqqs53j1bks46cbkq7ybigfyar")))) + (base32 "0ylsfr540l763bh010irbcavlskahyb1769pppimdgn22gyr3spk")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dt" ,r-dt) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-miniui" ,r-miniui) - ("r-nabor" ,r-nabor) - ("r-plotly" ,r-plotly) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsamtools" ,r-rsamtools) - ("r-rtsne" ,r-rtsne) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tfbstools" ,r-tfbstools))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-dt + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-matrix + r-miniui + r-nabor + r-plotly + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-rsamtools + r-rtsne + r-s4vectors + r-shiny + r-summarizedexperiment + r-tfbstools)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html") (synopsis "Determine chromatin variation across regions") (description @@ -12795,25 +13174,22 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "1bwdhx0ss0s8f4xdgwd7x48apn849x4dyb5hbyglcz31r5vh1qgz")))) + "01075vbs8hy399pxalav9rbkz4djvl84ip559jkz51fypd0m4i39")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-genomicranges" ,r-genomicranges) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/SingleCellExperiment") (synopsis "S4 classes for single cell data") (description "This package defines an S4 class for storing data from @@ -12823,32 +13199,64 @@ factors for each cell, along with the usual metadata for genes and libraries.") (license license:gpl3))) +(define-public r-singler + (package + (name "r-singler") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SingleR" version)) + (sha256 + (base32 "19lsn3cpghkhfbx4jqgbwwrnacrl7vj3r91ymd1gk02c9pn5dmci")))) + (properties `((upstream-name . "SingleR"))) + (build-system r-build-system) + (propagated-inputs + (list r-beachmat + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-matrix + r-rcpp + r-s4vectors + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/LTLA/SingleR") + (synopsis "Reference-based single-cell RNA-seq annotation") + (description + "This package performs unbiased cell type recognition from single-cell +RNA sequencing data, by leveraging reference transcriptomic datasets of pure +cell types to infer the cell of origin of each single cell independently.") + (license license:gpl3))) + (define-public r-scuttle (package (name "r-scuttle") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "015k879gg2r39lp6mz26jwmysa56k0ial6v74zzmbi8hnz9zic3i")))) + "1dbdb6yc6wk01dljy1vy6f0lf44crc5rxxnc4bhjk8i4iljz8467")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genomicranges" ,r-genomicranges) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biocgenerics + r-biocparallel + r-delayedarray + r-delayedmatrixstats + r-genomicranges + r-matrix + r-rcpp + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/scuttle") (synopsis "Single-cell RNA-Seq analysis utilities") (description @@ -12861,36 +13269,37 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "1046fgf93dda3y2z5ilrjdczz7klj67ag63p4p1h03965wpj9vfn")))) - (build-system r-build-system) - (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-matrix" ,r-matrix) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rtsne" ,r-rtsne) - ("r-s4vectors" ,r-s4vectors) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + "0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg")))) + (build-system r-build-system) + (propagated-inputs + (list r-beachmat + r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-ggbeeswarm + r-ggplot2 + r-ggrepel + r-gridextra + r-matrix + r-rcolorbrewer + r-rlang + r-rtsne + r-s4vectors + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/davismcc/scater") (synopsis "Single-cell analysis toolkit for gene expression data in R") (description "This package provides a collection of tools for doing @@ -12901,38 +13310,38 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.20.1") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0ilzp6ngw9pq88gk79iic2zxfh5jaic6lnq3xfwc9a269bjylff0")))) - (build-system r-build-system) - (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-bh" ,r-bh) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-bluster" ,r-bluster) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dqrng" ,r-dqrng) - ("r-edger" ,r-edger) - ("r-igraph" ,r-igraph) - ("r-limma" ,r-limma) - ("r-matrix" ,r-matrix) - ("r-metapod" ,r-metapod) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-statmod" ,r-statmod) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + "06lcxya6rpa8dv0il7m7fwyx0ci1y1jn16ff5lmvzf2mnr6q7lic")))) + (build-system r-build-system) + (propagated-inputs + (list r-beachmat + r-bh + r-biocgenerics + r-biocparallel + r-biocsingular + r-bluster + r-delayedarray + r-delayedmatrixstats + r-dqrng + r-edger + r-igraph + r-limma + r-matrix + r-metapod + r-rcpp + r-s4vectors + r-scuttle + r-singlecellexperiment + r-statmod + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/scran") (synopsis "Methods for single-cell RNA-Seq data analysis") (description "This package implements a variety of low-level analyses of @@ -12944,23 +13353,20 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0b22kzg751zlkcbs8pi0bcqrsj3imsg35qfvxfrqb7gav7qznc8v")))) + "0ifqj4a6mn4749sr62gq3dwd6mmbbzdx5mh5b5663vcgl1kw96x1")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-matrix r-matrixgenerics r-matrixstats r-rcpp)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/sparseMatrixStats/") (synopsis "Summary statistics for rows and columns of sparse matrices") (description @@ -12972,27 +13378,27 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.14.3") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1zxs2wjnsq9w1cl4andsd7y9xsdnl1an55khw9viaq758m7hhbcn")))) + "1pqwkk39rfhcnhmgchk0gfmm4jgasl19yq0nhhwsfj45y2vk6kjk")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-matrixstats" ,r-matrixstats) - ("r-s4vectors" ,r-s4vectors) - ("r-sparsematrixstats" ,r-sparsematrixstats))) + (list r-delayedarray + r-iranges + r-matrix + r-matrixgenerics + r-matrixstats + r-s4vectors + r-sparsematrixstats)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") (description @@ -13008,23 +13414,20 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "13g8a726vsyjs6m1kd42vf8avdnmhykxhl6z3j2njzkp2jg17pd8")))) + "1w8d1v2r3plwwcz23zhbpvklhapf2a6x3xmglyh4sh6sy9ynkgrv")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-clue" ,r-clue) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors))) + (list r-clue r-mass r-rcpp r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils") (synopsis "Core utils for mass spectrometry data") (description @@ -13037,24 +13440,53 @@ well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.") (license license:artistic2.0))) +(define-public r-msfeatures + (package + (name "r-msfeatures") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MsFeatures" version)) + (sha256 + (base32 "020ifrijlzdd3qk4bhd9z4knj5d87ildrkl3wcmxvwkvs9rbh8rq")))) + (properties `((upstream-name . "MsFeatures"))) + (build-system r-build-system) + (propagated-inputs + (list r-mscoreutils r-protgenerics r-summarizedexperiment)) + (native-inputs + (list r-knitr)) + (home-page "https://github.com/RforMassSpectrometry/MsFeatures") + (synopsis "Functionality for mass spectrometry features") + (description + "The MsFeature package defines functionality for Mass Spectrometry +features. This includes functions to group (LC-MS) features based on some of +their properties, such as retention time (coeluting features), or correlation +of signals across samples. This package hence can be used to group features, and +its results can be used as an input for the @code{QFeatures} package which +allows aggregating abundance levels of features within each group. This +package defines concepts and functions for base and common data types, +implementations for more specific data types are expected to be implemented in +the respective packages (such as e.g. @code{xcms}).") + (license license:artistic2.0))) + (define-public r-biocio (package (name "r-biocio") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "0skwnpxl6fkqihidpqrfzzh7b05x11j6jwkiinmhggmv0ggjb5ph")))) + "1qg6v961sbj7qwyjx4z720f6h0kq693p7gc8q99my7gqkbbcxrfr")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocIO") (synopsis "Standard input and output for Bioconductor packages") (description @@ -13074,21 +13506,18 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "0555a3riyp781mlffmnf93igfq8vl8wjk51pa9qb48qkdn6y8pfc")))) + "1jammjkjjkcqad2ki02l2pdf4jybyh71hv463aya2ylmzsin5vi9")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs - `(("r-gplots" ,r-gplots) - ("r-mass" ,r-mass) - ("r-msnbase" ,r-msnbase) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-gplots r-mass r-msnbase r-rcolorbrewer)) (home-page "https://bioconductor.org/packages/msmsEDA") (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts") @@ -13100,21 +13529,18 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "11vhy1l6za73dpdj85q4ksaghgd8vb2h8v9iirmsn2vpajqrvgjh")))) + "0xmjgd8rqpb8i7d46pvnj7da2di8bwfdncr48b8hgylkc98ghznb")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs - `(("r-edger" ,r-edger) - ("r-msmseda" ,r-msmseda) - ("r-msnbase" ,r-msnbase) - ("r-qvalue" ,r-qvalue))) + (list r-edger r-msmseda r-msnbase r-qvalue)) (home-page "https://bioconductor.org/packages/msmsTests") (synopsis "Differential LC-MS/MS expression tests") @@ -13132,45 +13558,45 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.16.2") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "1vw8x54hwgcyn29k81zcvawawy2iy2qgp49gjpb830q04gx6yc6h")))) + "15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-complexheatmap" ,r-complexheatmap) - ("r-consensusclusterplus" ,r-consensusclusterplus) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-drc" ,r-drc) - ("r-flowcore" ,r-flowcore) - ("r-flowsom" ,r-flowsom) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggridges" ,r-ggridges) - ("r-gridextra" ,r-gridextra) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-nnls" ,r-nnls) - ("r-purrr" ,r-purrr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-rtsne" ,r-rtsne) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-scater" ,r-scater) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-circlize + r-complexheatmap + r-consensusclusterplus + r-cowplot + r-data-table + r-dplyr + r-drc + r-flowcore + r-flowsom + r-ggplot2 + r-ggrepel + r-ggridges + r-gridextra + r-magrittr + r-matrix + r-matrixstats + r-nnls + r-purrr + r-rcolorbrewer + r-reshape2 + r-rtsne + r-s4vectors + r-scales + r-scater + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/HelenaLC/CATALYST") (synopsis "Cytometry data analysis tools") @@ -13190,32 +13616,32 @@ standards, ii) single-cell deconvolution, and iii) bead-based compensation.") (define-public r-erma (package (name "r-erma") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "02a9702sasgighwb0f9ii8n30ngfx1hjnppaay1f5zsigr8vqalz")))) + "0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicfiles + r-genomicranges + r-ggplot2 + r-homo-sapiens + r-iranges + r-rtracklayer + r-s4vectors + r-shiny + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/erma") (synopsis "Epigenomic road map adventures") (description @@ -13230,14 +13656,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0k3dxacrwgyrkvm7ggc2s1s1pbfs6c0a7ngykkj7jnc73czvnilx")))) + "1svmjaa3gisi39sl52337drvd54havcy5pjmwrykgykz5flid2m7")))) (build-system r-build-system) (arguments `(#:phases @@ -13250,35 +13676,35 @@ by Ernst and Kellis.") (("fechable") "fetchable")) #t))))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-organismdbi" ,r-organismdbi) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationfilter + r-biobase + r-biocgenerics + r-biostrings + r-biovizbase + r-bsgenome + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggally + r-ggplot2 + r-gridextra + r-gtable + r-hmisc + r-iranges + r-organismdbi + r-reshape2 + r-rlang + r-rsamtools + r-rtracklayer + r-s4vectors + r-scales + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "http://www.tengfei.name/ggbio/") (synopsis "Visualization tools for genomic data") (description @@ -13316,21 +13742,21 @@ interval to data view, mismatch pileup, and several splicing summaries.") (("importFrom\\(ff,.*") "import(ff)\n")) #t))))) (propagated-inputs - `(("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-biocgenerics" ,r-biocgenerics) - ("r-bit" ,r-bit) - ("r-doparallel" ,r-doparallel) - ("r-ff" ,r-ff) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-batchjobs + r-bbmisc + r-biocgenerics + r-bit + r-doparallel + r-ff + r-ffbase + r-foreach + r-genomicfiles + r-genomicranges + r-rtracklayer + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/gQTLBase") (synopsis "Infrastructure for eQTL, mQTL and similar studies") (description @@ -13353,38 +13779,38 @@ and more.") (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-beeswarm" ,r-beeswarm) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-erma" ,r-erma) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-gqtlbase" ,r-gqtlbase) - ("r-hardyweinberg" ,r-hardyweinberg) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-mgcv" ,r-mgcv) - ("r-plotly" ,r-plotly) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-snpstats" ,r-snpstats) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-batchjobs + r-bbmisc + r-beeswarm + r-biobase + r-biocgenerics + r-doparallel + r-dplyr + r-erma + r-ffbase + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicfiles + r-genomicranges + r-ggbeeswarm + r-ggplot2 + r-gqtlbase + r-hardyweinberg + r-homo-sapiens + r-iranges + r-limma + r-mgcv + r-plotly + r-reshape2 + r-s4vectors + r-shiny + r-snpstats + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/gQTLstats") (synopsis "Computationally efficient analysis for eQTL and allied studies") (description @@ -13398,41 +13824,41 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.36.2") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0lp0k8jd4dfsfn10706124graaqnzcyv1siblvm8dn2ykw2rc6vl")))) + "0nqa7m300d7gpsayb6c6rv64d3y8c390wvwgz7v29zs9c025s9a8")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-digest" ,r-digest) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-matrixstats" ,r-matrixstats) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biomart + r-biostrings + r-biovizbase + r-bsgenome + r-digest + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-lattice + r-latticeextra + r-matrixstats + r-rcolorbrewer + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/Gviz") (synopsis "Plotting data and annotation information along genomic coordinates") (description @@ -13447,30 +13873,30 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "0109cxsviq1sk5hfwkjzd0y1kpm934287asjjd0j8jhh4b0ah2b2")))) + "0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-readr" ,r-readr) - ("r-s4vectors" ,r-s4vectors) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) + (list r-annotationdbi + r-annotationhub + r-biocfilecache + r-biostrings + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-readr + r-s4vectors + r-snpstats + r-variantannotation)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/gwascat") (synopsis "Tools for data in the EMBL-EBI GWAS catalog") (description @@ -13481,20 +13907,17 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "0zxdph5hzr3kzj2g1mjqpiviwa189a5sq4bw7wiry6r79fdnklqs")))) + (base32 "1qqvbv1sq9j570syb2802ya2ffg1k8f1w986wr6ksqkwxb9qbbm4")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-rcurl" ,r-rcurl) - ("r-rgraphviz" ,r-rgraphviz) - ("r-xml" ,r-xml))) + (list r-graph r-rcurl r-rgraphviz r-xml)) (home-page "https://bioconductor.org/packages/KEGGgraph") (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor") (description @@ -13508,28 +13931,28 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "16vp5psmigxdkkd6fbivb6s8mvd7rsnm771wsbjvayl2y7ig7kq4")))) + "1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-httr" ,r-httr) - ("r-matrix" ,r-matrix) - ("r-rsamtools" ,r-rsamtools) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-ensdb-hsapiens-v75 + r-ensembldb + r-genomeinfodb + r-genomicfiles + r-httr + r-matrix + r-rsamtools + r-snpstats + r-variantannotation)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ldblock") (synopsis "Data structures for linkage disequilibrium measures in populations") (description @@ -13555,9 +13978,7 @@ defining LD blocks.") (properties `((upstream-name . "LDheatmap"))) (build-system r-build-system) (propagated-inputs - `(("r-genetics" ,r-genetics) - ("r-rcpp" ,r-rcpp) - ("r-snpstats" ,r-snpstats))) + (list r-genetics r-rcpp r-snpstats)) (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html") (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") (description @@ -13572,24 +13993,26 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "2.5-0") + (version "2.6-0") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw")))) + "0fr5pyc43hly5ry5bbygibbh9mnql7vl4r5qz42d0ry4hahyxa4w")))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-lme4" ,r-lme4) - ("r-nnet" ,r-nnet) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rjags" ,r-rjags))) + (list gsl)) + (propagated-inputs + (list r-doparallel + r-foreach + r-lme4 + r-nnet + r-rcpp + r-rcpparmadillo + r-rgraphviz + r-rjags)) (home-page "https://r-bayesian-networks.org/") (synopsis "Modelling multivariate data with additive bayesian networks") (description @@ -13619,12 +14042,9 @@ statistical dependencies in messy, complex data.") "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-catools" ,r-catools) - ("r-rcpp" ,r-rcpp) - ("r-rsamtools" ,r-rsamtools))) + (list r-bh r-catools r-rcpp r-rsamtools)) (home-page "https://cran.r-project.org/web/packages/spp/") (synopsis "ChIP-Seq processing pipeline") (description "This package provides tools for analysis of ChIP-seq and @@ -13634,24 +14054,24 @@ other functional sequencing data.") (define-public r-pathview (package (name "r-pathview") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "1fank0qavv9ikmzxvms8mky2wbzny02rfqkvsqzma26r3vl4r1g1")))) + (base32 "1jdl81lvrsz03b1nws90nssf2clipipzaqvwm1pq57mvshnlnkjr")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-graph" ,r-graph) - ("r-kegggraph" ,r-kegggraph) - ("r-keggrest" ,r-keggrest) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-png" ,r-png) - ("r-rgraphviz" ,r-rgraphviz) - ("r-xml" ,r-xml))) + (list r-annotationdbi + r-graph + r-kegggraph + r-keggrest + r-org-hs-eg-db + r-png + r-rgraphviz + r-xml)) (home-page "https://pathview.uncc.edu/") (synopsis "Tool set for pathway based data integration and visualization") (description @@ -13668,22 +14088,19 @@ large-scale and fully automated analysis.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "11vvih5y9kvyjfp2navkfpp4xiyfgwlv4r0x3p52hkj92pc2pg3g")))) + "0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-matrix" ,r-matrix) - ("r-survival" ,r-survival) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-biocgenerics r-matrix r-survival r-zlibbioc)) (home-page "https://bioconductor.org/packages/snpStats") (synopsis "Methods for SNP association studies") (description @@ -13695,32 +14112,32 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.18.0") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "09cqzylci4x4i7wn4ckcqhdlljbzfrp08wdvkkc5vrdldnj9pq5h")))) + "1akcmxzn4j9ph4n3lsgfh8fh8hrb28jjamz037w59bsdkcv6wyjq")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs - `(("r-bamsignals" ,r-bamsignals) - ("r-biocgenerics" ,r-biocgenerics) - ("r-chromstardata" ,r-chromstardata) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-mvtnorm" ,r-mvtnorm) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-bamsignals + r-biocgenerics + r-chromstardata + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-mvtnorm + r-reshape2 + r-rsamtools + r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ataudt/chromstaR") (synopsis "Chromatin state analysis for ChIP-Seq data") (description @@ -13733,27 +14150,27 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "1q4m6c5181dw12lvdp324jlk78c9jgcsg6b9hk87zjadp6j0gfr6")))) + "082yja4mmsq77sllv3c88agxjbb6jxwil2krb8fkfsijvyyx11c9")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dplyr" ,r-dplyr) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rtracklayer" ,r-rtracklayer))) + (list r-annotationdbi + r-dplyr + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-knitr + r-magrittr + r-rtracklayer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/Guitar") (synopsis "Visualize genomic features") (description @@ -13765,18 +14182,17 @@ starting site, start codon, stop codon and transcription ending site.") (define-public r-sushi (package (name "r-sushi") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "1m5l0nflhcynb3gz7b8qzvknb0s6xhds8z1yl3mbv8ic9qn2knv4")))) + "073mh1d063ph5zk1d8kipgblr4l1ixqbxflhq4669761fi2frlw4")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs - `(("r-biomart" ,r-biomart) - ("r-zoo" ,r-zoo))) + (list r-biomart r-zoo)) (home-page "https://bioconductor.org/packages/Sushi") (synopsis "Tools for visualizing genomics data") (description @@ -13787,28 +14203,28 @@ visualizations for publication-quality multi-panel figures.") (define-public r-ballgown (package (name "r-ballgown") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "0ff8z4pfgzai2q4aafclg36bhsi9jwl9xhh1p9fqhmikisscq7i1")))) + "0fiky82arvgzgxrm4bqn74m5kngqpdaqf6ks4cr89nlnhfq0v6rf")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-sva" ,r-sva))) + (list r-biobase + r-genomeinfodb + r-genomicranges + r-iranges + r-limma + r-rcolorbrewer + r-rtracklayer + r-s4vectors + r-sva)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ballgown") (synopsis "Flexible, isoform-level differential expression analysis") (description @@ -13821,27 +14237,27 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.2.3") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "0grgj7bzyqnxby0sx5ic1h9bzmx19xwl0a5b3v6wbnwqcla2i3kg")))) + "0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) - (inputs `(("megadepth" ,megadepth))) + (inputs (list megadepth)) (propagated-inputs - `(("r-cmdfun" ,r-cmdfun) - ("r-dplyr" ,r-dplyr) - ("r-fs" ,r-fs) - ("r-genomicranges" ,r-genomicranges) - ("r-magrittr" ,r-magrittr) - ("r-readr" ,r-readr) - ("r-xfun" ,r-xfun))) + (list r-cmdfun + r-dplyr + r-fs + r-genomicranges + r-magrittr + r-readr + r-xfun)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/LieberInstitute/megadepth") (synopsis "BigWig and BAM related utilities") (description @@ -13854,27 +14270,27 @@ regions or annotations of your choice from BigWig files.") (define-public r-beclear (package (name "r-beclear") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "0w18livng2gcmjgvws7pix3gsnj237rs34sgwxsfmn8p5vfx8b30")))) + "1njb1lfd4wmsrfw06jc8z8vdk14nmcw9lwyvbxr7z1zg4h8v6c29")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-biocparallel" ,r-biocparallel) - ("r-data-table" ,r-data-table) - ("r-futile-logger" ,r-futile-logger) - ("r-matrix" ,r-matrix) - ("r-outliers" ,r-outliers) - ("r-rcpp" ,r-rcpp) - ("r-rdpack" ,r-rdpack))) + (list r-abind + r-biocparallel + r-data-table + r-futile-logger + r-matrix + r-outliers + r-rcpp + r-rdpack)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/uds-helms/BEclear") (synopsis "Correction of batch effects in DNA methylation data") (description @@ -13887,34 +14303,34 @@ real numbers.") (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "1byciy7vzbdkdgaim10s9qb7zlxsywbhcsrka31gm0rm9ljqc665")))) + "0rbbl8m48qcvl26lnf27jq108p7pi84m9ac3qcpjc0ax5wywbv16")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs - `(("kallisto" ,kallisto) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-jsonlite" ,r-jsonlite) - ("r-rhdf5" ,r-rhdf5) - ("r-rslurm" ,r-rslurm) - ("r-rtracklayer" ,r-rtracklayer) - ("r-sjmisc" ,r-sjmisc) - ("r-tximport" ,r-tximport))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list kallisto + r-biomart + r-biostrings + r-data-table + r-dplyr + r-genomicfeatures + r-jsonlite + r-rhdf5 + r-rslurm + r-rtracklayer + r-sjmisc + r-tximport)) + (native-inputs (list r-knitr)) (home-page "https://github.com/BgeeDB/BgeeCall") (synopsis "RNA-Seq present/absent gene expression calls generation") (description - "BgeeCall allows to generate present/absent gene expression calls without + "BgeeCall allows generating present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee.") @@ -13923,29 +14339,29 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "1ziq180yfpdqwhjdzkwjjhwzn3kb0gkj6q0a26c7a30mcfb50w11")))) + "0pjymal01sjl5dc37g66wykgxnksarlbvwnbvhg7w0i7y92zavqk")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-curl" ,r-curl) - ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-graph" ,r-graph) - ("r-r-utils" ,r-r-utils) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-tidyr" ,r-tidyr) - ("r-topgo" ,r-topgo))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biobase + r-curl + r-data-table + r-digest + r-dplyr + r-graph + r-r-utils + r-rcurl + r-rsqlite + r-tidyr + r-topgo)) + (native-inputs (list r-knitr)) (home-page "https://github.com/BgeeDB/BgeeDB_R") (synopsis "Annotation and gene expression data retrieval from Bgee database") (description @@ -13957,22 +14373,19 @@ anatomical terms, mapped to genes by expression patterns.") (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "0pynx4ps1qxsn13ba6zyg6h5dqlp2y7qish67m7sdjns079zh061")))) + "0m9gx2g5ishbbh7aqp09mpknhr7q1v5ap0s6xp6ccj01pz2gkk8s")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs - `(("r-httpuv" ,r-httpuv) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-stringi" ,r-stringi))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-httpuv r-httr r-jsonlite r-stringi)) + (native-inputs (list r-knitr)) (home-page "https://github.com/tamerh/biobtreeR") (synopsis "Use biobtree tool from R") (description @@ -13984,18 +14397,18 @@ mappings functionalities.") (define-public r-minet (package (name "r-minet") - (version "3.50.0") + (version "3.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "0bir2zr4r2wawkdvdhrk2hcyxmgkrkfvx36jj85fcm24axlqrzzb")))) + "0nhgvgci4r9pjfsnvxyj2q8im1wvig4zmfx2kidw8f63x2ip2rbd")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs - `(("r-infotheo" ,r-infotheo))) + (list r-infotheo)) (home-page "http://minet.meyerp.com") (synopsis "Mutual information networks") (description @@ -14006,22 +14419,19 @@ information networks from data.") (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "1i1cavbbvxzqgqxfmikghnls18jrq12hb953mjrwa95lkhzdxm2d")))) + "1phyphdc1i55ab1a05633b0p41q8n7w0byp1plgcav2s3h8mk1km")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-e1071" ,r-e1071) - ("r-ebarrays" ,r-ebarrays) - ("r-minet" ,r-minet))) + (list r-biobase r-e1071 r-ebarrays r-minet)) (home-page "https://www.cicancer.org") (synopsis "Classify diseases and build gene networks using expression profiles") (description @@ -14034,18 +14444,18 @@ interface to query the classifier.") (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "05mk7iwzay1xrgvssbz7nyl5d1n03syalbk18lmjmbx05dy0cjik")))) + "1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) - (propagated-inputs `(("r-filelock" ,r-filelock))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-filelock)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/dir.expiry") (synopsis "Managing expiration for cache directories") (description @@ -14058,20 +14468,20 @@ eliminating obsolete caches generated by old versions of packages.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "0qbm6rj6h059hakflbwz4j4f59311jhbk5dnpx11kyixh5pgjk7v")))) + "0578rq2yz24sv7anb7vp0a0y35944ag1l8ca6haanb03wl97wm99")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) (propagated-inputs - `(("r-dir-expiry" ,r-dir-expiry))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-dir-expiry)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/basilisk.utils") (synopsis "Basilisk installation utilities") (description @@ -14082,21 +14492,19 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "1nzbn3f2jzvg3a3m6wgksi4cvamqas2q7csdk4ir7fcirasf536v")))) + "1cdkpngv9qybd9yxc3i2201p433vkkahs71v28x6lgs5l2wz3m1a")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs - `(("r-basilisk-utils" ,r-basilisk-utils) - ("r-dir-expiry" ,r-dir-expiry) - ("r-reticulate" ,r-reticulate))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-basilisk-utils r-dir-expiry r-reticulate)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/basilisk") (synopsis "Freeze Python dependencies inside Bioconductor packages") (description @@ -14110,24 +14518,29 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "08awghsg7q22csb0j9dr8dpb1vkn9gcs9qnhhljxifkw2ahbqia4")))) + "0kh5lmv992v4r5r58x29403cll0zxr9fx4ar81nrzvnch5668v39")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) - ("r-fs" ,r-fs) - ("r-glue" ,r-glue) - ("r-rlang" ,r-rlang) - ("r-styler" ,r-styler) - ("r-usethis" ,r-usethis))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocmanager + r-fs + r-glue + r-rlang + r-styler + r-usethis)) + (native-inputs (list r-knitr)) (home-page "https://github.com/lcolladotor/biocthis") (synopsis "Automate package and project setup for Bioconductor packages") (description @@ -14139,25 +14552,25 @@ Bioconductor-friendly.") (define-public r-biocdockermanager (package (name "r-biocdockermanager") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocDockerManager" version)) (sha256 (base32 - "0dh1flm5chsdcihljrg6znjskqkp0qyjh39hsv4zq0frf1rm97j7")))) + "1kpdmpcngnl667bfffp9bkf8c31ipmhsncq0h9bf3a4k8b83pi0w")))) (properties `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) (propagated-inputs - `(("docker" ,docker) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-memoise" ,r-memoise) - ("r-readr" ,r-readr) - ("r-whisker" ,r-whisker))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list docker + r-dplyr + r-httr + r-memoise + r-readr + r-whisker)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocDockerManager") (synopsis "Access and manage Bioconductor Docker images") (description @@ -14169,35 +14582,36 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.0.4") + (version "1.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "1apnbr5p619nsrhd2drm6arj69sw0wijv8ap7dfrndqkffrpbfmx")))) + "0b5zva16r4kz8736h3djjgmh35nxmlin4f374rb4i2s55zsrb638")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs - `(("r-chk" ,r-chk) - ("r-jsonlite" ,r-jsonlite) - ("r-lgr" ,r-lgr) - ("r-lifecycle" ,r-lifecycle) - ("r-openssl" ,r-openssl) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-r6" ,r-r6) - ("r-rappdirs" ,r-rappdirs) - ("r-rcpp" ,r-rcpp) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-stringr" ,r-stringr) - ("r-testthat" ,r-testthat) - ("r-withr" ,r-withr) - ("r-xml" ,r-xml) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocfilecache + r-chk + r-jsonlite + r-lgr + r-lifecycle + r-openssl + r-plyr + r-progress + r-r6 + r-rappdirs + r-rcpp + r-rcurl + r-rsqlite + r-stringr + r-testthat + r-withr + r-xml + r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biodb") (synopsis "Library for connecting to chemical and biological databases") (description @@ -14213,22 +14627,19 @@ separate published packages.") (define-public r-biomformat (package (name "r-biomformat") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "1wgshkddxbmpsihpkm0dp7vqp59ns6iqbx574y80n2pxb8dx8sy9")))) + "0xf99j4lhf8kh9h1317hrbzxdv6rljs1fn68r8s40x6y4db3l817")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs - `(("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-rhdf5" ,r-rhdf5))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-jsonlite r-matrix r-plyr r-rhdf5)) + (native-inputs (list r-knitr)) (home-page "https://github.com/joey711/biomformat/") (synopsis "Interface package for the BIOM file format") (description @@ -14245,14 +14656,14 @@ as extensions of common core functions/methods.") (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "1di7y10mr7caacd6igwxnr62cm4v1x877yi4a2i5jqz1058jqni7")))) + "088gzh33vjkjf78xczqfs89pyg0k7c3533yfvijqxl84ni2ky78z")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") @@ -14265,21 +14676,18 @@ design.") (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "04pld93nffbci47dnf0awmcmhlfzv599ggcd7hvq78w41ac60qv8")))) + "0jqgazwz35gz11a7vzanyy2yalzalx0z0rw6y18nmk8dbv01nv2j")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-graph" ,r-graph) - ("r-mvcclass" ,r-mvcclass) - ("r-rgraphviz" ,r-rgraphviz))) + (list r-biobase r-graph r-mvcclass r-rgraphviz)) (home-page "https://bioconductor.org/packages/BioMVCClass") (synopsis "Model-View-Controller (MVC) classes that use Biobase") (description @@ -14290,21 +14698,18 @@ design.") (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "0wyzj422smr4m9mswzn9inc1sn86pnia7jmd6k28nd2a7fjyrm16")))) + "01nhjhfyzs67p97bk9bjqdxk239ckl8sgfj55azk1zmw92aw2hfy")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-genomicranges r-gviz r-iranges r-mvtnorm)) (home-page "https://bioconductor.org/packages/biomvRCNS") (synopsis "Copy number study and segmentation for multivariate biological data") (description @@ -14318,39 +14723,39 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.0.4") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "1yj0pavyfrj2gsvaj1dkgmznibm2appxjx9rk5qjslhslmm5b05b")))) + "0ddrzv1g46hvm52dzrcj5nbyyw9a16cqk8zg20wnkrh3qw1h4d9p")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-complexheatmap" ,r-complexheatmap) - ("r-deseq2" ,r-deseq2) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-genie3" ,r-genie3) - ("r-ggnetwork" ,r-ggnetwork) - ("r-ggnewscale" ,r-ggnewscale) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-igraph" ,r-igraph) - ("r-intergraph" ,r-intergraph) - ("r-matrixstats" ,r-matrixstats) - ("r-minet" ,r-minet) - ("r-netrep" ,r-netrep) - ("r-networkd3" ,r-networkd3) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-sva" ,r-sva) - ("r-wgcna" ,r-wgcna))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-complexheatmap + r-deseq2 + r-dynamictreecut + r-genie3 + r-ggnetwork + r-ggnewscale + r-ggplot2 + r-ggpubr + r-igraph + r-intergraph + r-matrixstats + r-minet + r-netrep + r-networkd3 + r-rcolorbrewer + r-reshape2 + r-summarizedexperiment + r-sva + r-wgcna)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/almeidasilvaf/BioNERO") (synopsis "Biological network reconstruction omnibus") (description @@ -14374,22 +14779,18 @@ networks.") (define-public r-bionet (package (name "r-bionet") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "15rk1jfv4h1mxvr5bs0qmq6fdnza7zcmksigqxb46fs7f6znr3yi")))) + "05rj14jn4gn0hfn57amf19b8fqwkd3y2ji3mg7m1yg1w7n4qxqsg")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-graph" ,r-graph) - ("r-igraph" ,r-igraph) - ("r-rbgl" ,r-rbgl))) + (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl)) (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html") (synopsis "Functional analysis of biological networks") (description @@ -14407,37 +14808,37 @@ scoring subnetwork.") (define-public r-bionetstat (package (name "r-bionetstat") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNetStat" version)) (sha256 (base32 - "16xlfng9m8xvm831c2x6zmjc0gavlfiy9pnza55hdv86888fcnbg")))) + "13br8x4809hrr4ibz6iy5qjza9j6cazmkpvfikvw6bs588csxwf8")))) (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-igraph" ,r-igraph) - ("r-knitr" ,r-knitr) - ("r-markdown" ,r-markdown) - ("r-pathview" ,r-pathview) - ("r-pheatmap" ,r-pheatmap) - ("r-plyr" ,r-plyr) - ("r-psych" ,r-psych) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rjsonio" ,r-rjsonio) - ("r-rmarkdown" ,r-rmarkdown) - ("r-shiny" ,r-shiny) - ("r-shinybs" ,r-shinybs) - ("r-whisker" ,r-whisker) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-dt + r-ggplot2 + r-hmisc + r-igraph + r-knitr + r-markdown + r-pathview + r-pheatmap + r-plyr + r-psych + r-rcolorbrewer + r-rjsonio + r-rmarkdown + r-shiny + r-shinybs + r-whisker + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/jardimViniciusC/BioNetStat") (synopsis "Biological network analysis") (description @@ -14449,22 +14850,20 @@ network and metabolic pathways view.") (define-public r-bioqc (package (name "r-bioqc") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "04akp94p0d0zid55m1b1k3qlw7iq914pcg57lihgj3pa92n1sc5l")))) + "190336qk0plg79gzvfn6wfplsi8nq0nj8508g7m0w3z6bdgwy407")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-edger" ,r-edger) - ("r-rcpp" ,r-rcpp))) + (list r-biobase r-edger r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://accio.github.io/BioQC/") (synopsis "Detect tissue heterogeneity in expression profiles with gene sets") (description @@ -14477,26 +14876,26 @@ optimised for high performance.") (define-public r-biotip (package (name "r-biotip") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 - "1i6r8px0fmdjx8frpljppwql74mhx08ibvhs9y3qk91ck5h3f0js")))) + "0xmy5c4i9gf6d04gara6lbnnldqmzjaascb2pd2ih60jw2mvl4ys")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-genomicranges" ,r-genomicranges) - ("r-hmisc" ,r-hmisc) - ("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-psych" ,r-psych) - ("r-stringr" ,r-stringr))) + (list r-cluster + r-genomicranges + r-hmisc + r-igraph + r-mass + r-psych + r-stringr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/xyang2uchicago/BioTIP") (synopsis "R package for characterization of biological tipping-point") (description @@ -14507,33 +14906,31 @@ help unravel disease regulatory trajectory.") (define-public r-biotmle (package (name "r-biotmle") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "01smkmbv40yprgrgi2gjnmi8ncqyrlkfdxsh33ki20amcx32nc7f")))) + "0p3iavf9059qa8qvfvqzskfc5gki3z0ivkkqdwg5anvf0wv2k47g")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-dofuture" ,r-dofuture) - ("r-dplyr" ,r-dplyr) - ("r-drtmle" ,r-drtmle) - ("r-future" ,r-future) - ("r-ggplot2" ,r-ggplot2) - ("r-ggsci" ,r-ggsci) - ("r-limma" ,r-limma) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-superheat" ,r-superheat) - ("r-tibble" ,r-tibble))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-biocgenerics + r-biocparallel + r-dplyr + r-drtmle + r-ggplot2 + r-ggsci + r-limma + r-s4vectors + r-summarizedexperiment + r-superheat + r-tibble)) + (native-inputs + (list r-knitr)) (home-page "https://code.nimahejazi.org/biotmle/") (synopsis "Targeted learning with moderated statistics for biomarker discovery") (description @@ -14551,42 +14948,42 @@ ensemble machine learning for the estimation of nuisance functions.") (define-public r-bsseq (package (name "r-bsseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "1xpv85hr681kkkilsnasndkszwmzbzq11y0lff4na2ilsm7sqmmi")))) + "1i30zf6457a0qd64s89x9l544y1h0hj9rfgf1m8l4krd487a9b9d")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-hdf5array" ,r-hdf5array) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-permute" ,r-permute) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5" ,r-rhdf5) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-data-table + r-delayedarray + r-delayedmatrixstats + r-genomeinfodb + r-genomicranges + r-gtools + r-hdf5array + r-iranges + r-limma + r-locfit + r-permute + r-r-utils + r-rcpp + r-rhdf5 + r-s4vectors + r-scales + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/hansenlab/bsseq") (synopsis "Analyze, manage and store bisulfite sequencing data") (description @@ -14597,36 +14994,36 @@ visualizing bisulfite sequencing data.") (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "1jbbjifjsnk9261wqmdwkbzj1w52g6vaanpk4w816ri0fap587m4")))) + "1d6y6rbvcgprmzqkdzxg5csf0yv845d9vw10pcd1pzyndrama1vd")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-annotatr" ,r-annotatr) - ("r-biocparallel" ,r-biocparallel) - ("r-bsseq" ,r-bsseq) - ("r-bumphunter" ,r-bumphunter) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-locfit" ,r-locfit) - ("r-matrixstats" ,r-matrixstats) - ("r-nlme" ,r-nlme) - ("r-outliers" ,r-outliers) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationhub + r-annotatr + r-biocparallel + r-bsseq + r-bumphunter + r-delayedmatrixstats + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-locfit + r-matrixstats + r-nlme + r-outliers + r-rcolorbrewer + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/dmrseq") (synopsis "Detection and inference of differentially methylated regions") (description @@ -14643,13 +15040,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.0.4") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "0rbq3h3cp5dgpy5ifmbnfm6z8w4jv45wjzyl1f4qacgrbyf2l30a")))) + (base32 "1q89mxnp8cig9r1499g7fb9p9x9ryz1dmc3w6ps5ww9n6rl8jqk8")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -14658,29 +15055,30 @@ interest on transformed methylation proportions.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-curl" ,r-curl) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-igraph" ,r-igraph) - ("r-jsonlite" ,r-jsonlite) - ("r-later" ,r-later) - ("r-logger" ,r-logger) - ("r-magrittr" ,r-magrittr) - ("r-progress" ,r-progress) - ("r-purrr" ,r-purrr) - ("r-rappdirs" ,r-rappdirs) - ("r-readr" ,r-readr) - ("r-readxl" ,r-readxl) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-checkmate + r-crayon + r-curl + r-digest + r-dplyr + r-httr + r-igraph + r-jsonlite + r-later + r-logger + r-magrittr + r-progress + r-purrr + r-rappdirs + r-readr + r-readxl + r-rlang + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-xml2 + r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://saezlab.github.io/OmnipathR/") (synopsis "OmniPath web service client and more") (description @@ -14694,45 +15092,45 @@ for ligand activity prediction from transcriptomics data.") (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "0f4kk4v2c5diq0fbvyvgwjd1kjk9izr6n9wfrlrr7wbx4pz3c3h6")))) + "16ds322b21g8ys5c3lkrvi70i82f9rxvnknbiqx4sp6f2l01j5yj")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biscuiteerdata" ,r-biscuiteerdata) - ("r-bsseq" ,r-bsseq) - ("r-data-table" ,r-data-table) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dmrseq" ,r-dmrseq) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-hdf5array" ,r-hdf5array) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-impute" ,r-impute) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mus-musculus" ,r-mus-musculus) - ("r-qdnaseq" ,r-qdnaseq) - ("r-qualv" ,r-qualv) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-biscuiteerdata + r-bsseq + r-data-table + r-delayedmatrixstats + r-dmrseq + r-genomeinfodb + r-genomicranges + r-gtools + r-hdf5array + r-homo-sapiens + r-impute + r-matrix + r-matrixstats + r-mus-musculus + r-qdnaseq + r-qualv + r-r-utils + r-readr + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/trichelab/biscuiteer") (synopsis "Convenience functions for the Biscuit package") (description @@ -14742,37 +15140,92 @@ samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.") (license license:gpl3))) +(define-public r-tcgabiolinks + (package + (name "r-tcgabiolinks") + (version "2.22.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TCGAbiolinks" version)) + (sha256 + (base32 "0l7hfwgd8aiqv2k98jchkr3sdp9hwdg7pzm3bnvr6k7p93ifr6wc")))) + (properties `((upstream-name . "TCGAbiolinks"))) + (build-system r-build-system) + (propagated-inputs + (list r-biomart + r-data-table + r-downloader + r-dplyr + r-genomicranges + r-ggplot2 + r-httr + r-iranges + r-jsonlite + r-knitr + r-plyr + r-purrr + r-r-utils + r-readr + r-rvest + r-s4vectors + r-stringr + r-summarizedexperiment + r-tcgabiolinksgui-data + r-tibble + r-tidyr + r-xml + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks") + (synopsis "Integrative analysis with GDC data") + (description + "The aim of TCGAbiolinks is: + +@enumerate +@item facilitate GDC open-access data retrieval; +@item prepare the data using the appropriate pre-processing strategies; +@item provide the means to carry out different standard analyses, and; +@item to easily reproduce earlier research results. +@end enumerate + +In more detail, the package provides multiple methods for analysis (e.g., +differential expression analysis, identifying differentially methylated +regions) and methods for visualization (e.g., survival plots, volcano plots, +starburst plots) in order to easily develop complete analysis pipelines.") + (license license:gpl3+))) + (define-public r-tximeta (package (name "r-tximeta") - (version "1.10.0") + (version "1.12.4") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "0ipgpcl93cac4qff6lp9x2l3gav5kb1x1d56g32h09hlm797rvvh")))) + "1lm2r64d6sdfzvxcabgs0214cdc5dl9pfx562acjcxz5mb101g9g")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biostrings" ,r-biostrings) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble) - ("r-tximport" ,r-tximport))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationhub + r-biocfilecache + r-biostrings + r-ensembldb + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-jsonlite + r-matrix + r-s4vectors + r-summarizedexperiment + r-tibble + r-tximport)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/mikelove/tximeta") (synopsis "Transcript quantification import with automatic metadata") (description @@ -14782,3 +15235,41 @@ and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.") (license license:gpl2))) + +(define-public r-phyloseq + (package + (name "r-phyloseq") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "phyloseq" version)) + (sha256 + (base32 "0k0aj8f7g1vr7l0qcc507b3w67zc1k9x7sdblm7mjb20zqr3916s")))) + (properties `((upstream-name . "phyloseq"))) + (build-system r-build-system) + (propagated-inputs + (list r-ade4 + r-ape + r-biobase + r-biocgenerics + r-biomformat + r-biostrings + r-cluster + r-data-table + r-foreach + r-ggplot2 + r-igraph + r-multtest + r-plyr + r-reshape2 + r-scales + r-vegan)) + (native-inputs + (list r-knitr)) + (home-page "https://github.com/joey711/phyloseq") + (synopsis "Handling and analysis of high-throughput microbiome census data") + (description + "Phyloseq provides a set of classes and tools to facilitate the import, +storage, analysis, and graphical display of microbiome census data.") + (license license:agpl3))) |