diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 4986 |
1 files changed, 4326 insertions, 660 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 171736064c..4cbffac000 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,15 +1,16 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> -;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 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 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019, 2020, 2021 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> ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,8 +36,11 @@ #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression) + #:use-module (gnu packages curl) + #:use-module (gnu packages docker) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) @@ -81,6 +85,31 @@ submit gene-specific information, or which are scheduled for intense sequence analysis.") (license license:artistic2.0))) +(define-public r-org-bt-eg-db + (package + (name "r-org-bt-eg-db") + (version "3.13.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri + "org.Bt.eg.db" + version + 'annotation)) + (sha256 + (base32 + "0pwvwyfah8fhvaxdc8zkp3lp1v4mchhzr84r3hb0jx97icdvhafi")))) + (properties `((upstream-name . "org.Bt.eg.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/org.Bt.eg.db") + (synopsis "Genome wide annotation for Bovine") + (description + "This package provides genome wide annotations for Bovine, primarily +based on mapping using Entrez Gene identifiers.") + (license license:artistic2.0))) + (define-public r-reactome-db (package (name "r-reactome-db") @@ -103,6 +132,29 @@ analysis.") database, assembled using data from REACTOME.") (license license:cc-by4.0))) +(define-public r-bsgenome-btaurus-ucsc-bostau8 + (package + (name "r-bsgenome-btaurus-ucsc-bostau8") + (version "1.4.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Btaurus.UCSC.bosTau8" + version 'annotation)) + (sha256 + (base32 + "16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6")))) + (properties + `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome))) + (home-page + "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/") + (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)") + (description "This package provides the full genome sequences for Bos +taurus (UCSC version bosTau8).") + (license license:artistic2.0))) + (define-public r-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") @@ -412,6 +464,28 @@ in Biostrings objects.") ID and species. It is used by functions in the GenomeInfoDb package.") (license license:artistic2.0))) +(define-public r-go-db + (package + (name "r-go-db") + (version "3.7.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GO.db" version 'annotation)) + (sha256 + (base32 + "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5")))) + (properties + `((upstream-name . "GO.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/GO.db") + (synopsis "Annotation maps describing the entire Gene Ontology") + (description + "The purpose of this GO.db annotation package is to provide detailed +information about the latest version of the Gene Ontologies.") + (license license:artistic2.0))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") @@ -439,6 +513,34 @@ ID and species. It is used by functions in the GenomeInfoDb package.") several related annotation packages.") (license license:artistic2.0))) +(define-public r-mus-musculus + (package + (name "r-mus-musculus") + (version "1.3.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Mus.musculus" version 'annotation)) + (sha256 + (base32 + "143zdf83gbfqhy8jm9df7gzhw5q3a64jrjrxrzjf0zd76j8s8j6y")))) + (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))) + (home-page "https://bioconductor.org/packages/Mus.musculus") + (synopsis "Annotation package for the Mus.musculus object") + (description + "This package contains the @code{Mus.musculus} object to access data +from several related annotation packages.") + (license license:artistic2.0))) + (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") @@ -934,6 +1036,64 @@ datasets which are derived from the Allen Brain Atlas: All datasets are restricted to protein coding genes.") (license license:gpl2+))) +(define-public r-aneufinderdata + (package + (name "r-aneufinderdata") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AneuFinderData" version 'experiment)) + (sha256 + (base32 + "02vb3kmza5hv8bc424fdmfif608xvpdb759w8882kac8izpv29ks")))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/AneuFinderData/") + (synopsis "Data package for @code{AneuFinder}") + (description "This package contains data used by @code{AneuFinder}.") + (license license:artistic2.0))) + +(define-public r-aneufinder + (package + (name "r-aneufinder") + (version "1.20.0") + (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))) + (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 +calling, plotting, export and analysis from whole-genome single cell +sequencing data.") + (license license:artistic2.0))) + (define-public r-arrmdata (package (name "r-arrmdata") @@ -954,6 +1114,32 @@ All datasets are restricted to protein coding genes.") from Illumina 450k methylation arrays.") (license license:artistic2.0))) +(define-public r-biscuiteerdata + (package + (name "r-biscuiteerdata") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biscuiteerData" version 'experiment)) + (sha256 + (base32 + "1d7zibjf0qccmdnzdxh7wy1h943yhnbf8zdix72486pvhzm124zj")))) + (properties + `((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))) + (home-page "https://bioconductor.org/packages/biscuiteerData") + (synopsis "Data package for Biscuiteer") + (description + "This package contains default datasets used by the Bioconductor package +biscuiteer.") + (license license:gpl3))) + (define-public r-chromstardata (package (name "r-chromstardata") @@ -974,6 +1160,30 @@ from Illumina 450k methylation arrays.") chromstaR package.") (license license:gpl3))) +(define-public r-copyhelper + (package + (name "r-copyhelper") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CopyhelpeR" version 'experiment)) + (sha256 + (base32 + "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) + (properties `((upstream-name . "CopyhelpeR"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/CopyhelpeR/") + (synopsis "Helper files for CopywriteR") + (description + "This package contains the helper files that are required to run the +Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content +and mappability files for the reference genomes hg18, hg19, hg38, mm9 and +mm10. In addition, it contains a blacklist filter to remove regions that +display copy number variation. Files are stored as GRanges objects from the +GenomicRanges Bioconductor package.") + (license license:gpl2))) + (define-public r-genelendatabase (package (name "r-genelendatabase") @@ -998,6 +1208,32 @@ chromstaR package.") genomes and gene ID formats, largely based on the UCSC table browser.") (license license:lgpl2.0+))) +(define-public r-genomationdata + (package + (name "r-genomationdata") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "genomationData" version 'experiment)) + (sha256 + (base32 + "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g")))) + (properties + `((upstream-name . "genomationData"))) + (build-system r-build-system) + ;; As this package provides little more than large data files, it doesn't + ;; make sense to build substitutes. + (arguments `(#:substitutable? #f)) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") + (synopsis "Experimental data for use with the genomation package") + (description + "This package contains experimental genetic data for use with the +genomation package. Included are Chip Seq, Methylation and Cage data, +downloaded from Encode.") + (license license:gpl3+))) + (define-public r-pasilla (package (name "r-pasilla") @@ -1165,14 +1401,14 @@ across the entire multi-'omics experiment.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.12.0") + (version "3.13.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk")))) + "0rsw8g4g1pcjw1zbx8x17yd3drhxqk4sx3cy3ddzy5731hl6mbfi")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -1185,13 +1421,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.36.0") + (version "0.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q")))) + "1kv7lzmyki3hi771v01nml1v1hzz8pyhqqv0xcdzqy354mlgx4m6")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -1205,13 +1441,13 @@ packages.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj")))) + "1xhirbjdw09cqm4xvysxqicvqjbahavwvs7shg4cb05gwyd2ha8g")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) @@ -1232,13 +1468,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj")))) + "1avvmvrmldbscc7xd6a6k22xjykbzafvqf87wh5z9rx3qlzswsjx")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -1259,16 +1495,76 @@ data. In addition, provides numerous plotting functions for commonly used visualizations.") (license license:artistic2.0))) +(define-public r-decipher + (package + (name "r-decipher") + (version "2.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DECIPHER" version)) + (sha256 + (base32 + "0mr7glkx2d37l9nszs52m0kycpm14vxl5gdp3z7i5j7yig1sw2nk")))) + (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))) + (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 +biological sequences.") + (license license:gpl3))) + +(define-public r-deepsnv + (package + (name "r-deepsnv") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "deepSNV" version)) + (sha256 + (base32 + "0zz56hf417m7bgg2g2wpbaik30pi6h2nam1n5bviqgdn4mv8n0bs")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/gerstung-lab/deepSNV/") + (synopsis "Detection of subclonal SNVs in deep sequencing data") + (description + "This package provides quantitative variant callers for detecting +subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. +The deepSNV algorithm is used for a comparative setup with a control experiment +of the same loci and uses a beta-binomial model and a likelihood ratio test to +discriminate sequencing errors and subclonal SNVs. The shearwater algorithm +computes a Bayes classifier based on a beta-binomial model for variant calling +with multiple samples for precisely estimating model parameters - such as local +error rates and dispersion - and prior knowledge, e.g. from variation data +bases such as COSMIC.") + (license license:gpl3))) + (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.16.3") + (version "0.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0w1wppy6m2iv41852dscg3y19sq84ahdx3m7c2p2pxjcznmv6hys")))) + "0w632262dqzcnvq9s6jvc7naz93dayx51fsv05s0zb6cjwygbqjr")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -1295,18 +1591,19 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-bluster (package (name "r-bluster") - (version "1.0.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61")))) + "128zd5vwlhmrkq0bpp1dxnkrcqfz1mjmdjlla4wqbjv7v6yyn6lg")))) (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) @@ -1324,13 +1621,13 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq")))) + "17sx0v5lq2zmg098ps4ksj1h0yla3vlh6s2w1ahqsq0nvm193scm")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -1348,13 +1645,13 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-iranges (package (name "r-iranges") - (version "2.24.1") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) + "0dzj8wqbjzilh2dsaj3ylx958xqrv0c688ayfq2r1z7rs75qy7kx")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -1406,18 +1703,20 @@ absolute GSEA.") (define-public r-bisquerna (package (name "r-bisquerna") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "BisqueRNA" version)) (sha256 (base32 - "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) + "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n")))) (properties `((upstream-name . "BisqueRNA"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-limsolve" ,r-limsolve))) + (native-inputs + `(("r-knitr" ,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 @@ -1501,17 +1800,45 @@ optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.") (license license:gpl2+))) +(define-public r-affy + (package + (name "r-affy") + (version "1.70.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affy" version)) + (sha256 + (base32 + "0vz5y92gqcm0qk57qlba85bk683lzdr7vkmxv109rq6i17vdkkrm")))) + (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))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://bioconductor.org/packages/affy") + (synopsis "Methods for affymetrix oligonucleotide arrays") + (description + "This package contains functions for exploratory oligonucleotide array +analysis.") + (license license:lgpl2.0+))) + (define-public r-affycomp (package (name "r-affycomp") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk")))) + "07my5scdh6h0y1bx1h9y5m4fa8bnmw389f83gkb7cf19w4vp36b2")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) @@ -1525,14 +1852,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x")))) + "1xwz22wf2smsvmd0d5lfadbsgscnl3fl9msypy2mml38k048p6vj")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) @@ -1553,14 +1880,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b")))) + "0242ga68wrdk1kcmxfdbq73a0d3zhrzdlzkzphfg3q0zjbvg49jj")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -1578,14 +1905,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0")))) + "1dx861spr3kn1dxwhf43s5l1r7bmrq0h6538l3q64iiwzzc6krdh")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -1617,17 +1944,41 @@ problems in CEL-level data to help evaluate performance of quality metrics.") to streamline the more common analyses that a Biostatistician might see.") (license license:artistic2.0))) +(define-public r-affyio + (package + (name "r-affyio") + (version "1.62.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affyio" version)) + (sha256 + (base32 + "07kibqsm888g06qqqa4648ph877kriy74kprbri8nyx83y8aspjr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-zlibbioc" ,r-zlibbioc))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/bmbolstad/affyio") + (synopsis "Tools for parsing Affymetrix data files") + (description + "This package provides routines for parsing Affymetrix data files based +upon file format information. The primary focus is on accessing the CEL and +CDF file formats.") + (license license:lgpl2.0+))) + (define-public r-affxparser (package (name "r-affxparser") - (version "1.62.0") + (version "1.64.1") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p")))) + "0lr0kmp087j2g4i5kd7rh8a038ymp6z82861lyql2fwk5dh80043")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -1648,14 +1999,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l")))) + "13ny596wh65sw7dbw0zd4h84d6k1w99g91c4sqy83mdzgpv73sz7")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -1675,13 +2026,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.52.0") + (version "1.54.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) + "0fcammls431pgmp47r85k0zh3bz42bajbqdmafd31kpqncc1ijal")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -1689,6 +2040,7 @@ microarrays.") `(("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))) @@ -1701,17 +2053,43 @@ microarrays.") annotation data packages using SQLite data storage.") (license license:artistic2.0))) +(define-public r-annotationfilter + (package + (name "r-annotationfilter") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationFilter" version)) + (sha256 + (base32 + "0799jja6v7l3jsi26wbjalkr5lriaxid05xb5g36iq93myhaj0sa")))) + (properties + `((upstream-name . "AnnotationFilter"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicranges" ,r-genomicranges) + ("r-lazyeval" ,r-lazyeval))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/Bioconductor/AnnotationFilter") + (synopsis "Facilities for filtering Bioconductor annotation resources") + (description + "This package provides classes and other infrastructure to implement +filters for manipulating Bioconductor annotation resources. The filters are +used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") + (license license:artistic2.0))) + (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7")))) + "1by3diy0y4809k97cw97mp4j177gn1dzhqil8myij1r7b8sk7hax")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -1733,16 +2111,114 @@ annotation data packages using SQLite data storage.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-annotationhub + (package + (name "r-annotationhub") + (version "3.0.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationHub" version)) + (sha256 + (base32 + "12i8lafy1z97gs4knqi7r5l1hd7dr6j8a23qj4fkdpqsdpyz21z7")))) + (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))) + (home-page "https://bioconductor.org/packages/AnnotationHub") + (synopsis "Client to access AnnotationHub resources") + (description + "This package provides a client for the Bioconductor AnnotationHub web +resource. The AnnotationHub web resource provides a central location where +genomic files (e.g. VCF, bed, wig) and other resources from standard +locations (e.g. UCSC, Ensembl) can be discovered. The resource includes +metadata about each resource, e.g., a textual description, tags, and date of +modification. The client creates and manages a local cache of files retrieved +by the user, helping with quick and reproducible access.") + (license license:artistic2.0))) + +(define-public r-aroma-light + (package + (name "r-aroma-light") + (version "3.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "aroma.light" version)) + (sha256 + (base32 + "1yvq6l1p8cpijvlib4fn9y88ihn0gaalrmgx82jgrfmnszkqn3y5")))) + (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))) + (home-page "https://github.com/HenrikBengtsson/aroma.light") + (synopsis "Methods for normalization and visualization of microarray data") + (description + "This package provides methods for microarray analysis that take basic +data types such as matrices and lists of vectors. These methods can be used +standalone, be utilized in other packages, or be wrapped up in higher-level +classes.") + (license license:gpl2+))) + +(define-public r-bamsignals + (package + (name "r-bamsignals") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bamsignals" version)) + (sha256 + (base32 + "1ljrip0jlxjcljqac7vzvwqbcqil5v4f4s4bhpq4akvdkshas6mn")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/bamsignals") + (synopsis "Extract read count signals from bam files") + (description + "This package efficiently obtains count vectors from indexed bam +files. It counts the number of nucleotide sequence reads in given genomic +ranges and it computes reads profiles and coverage profiles. It also handles +paired-end data.") + (license license:gpl2+))) + (define-public r-biobase (package (name "r-biobase") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) + "1sg8w8860zhlz9s1pf75xa8asd2hyqsj13fh5xc37hf5yqdfkavr")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -1758,21 +2234,21 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.46.3") + (version "2.48.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) + "096s243yzbhhz3wsm7azml5sznqczmcpi5g0gnb02mah1przczfx")))) (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-openssl" ,r-openssl) ("r-progress" ,r-progress) ("r-rappdirs" ,r-rappdirs) ("r-stringr" ,r-stringr) @@ -1796,13 +2272,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.24.1") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) + "1y459cygq21f3igsdlxz1zlyad8qbl2qlr5h2d2dpnvblykvf48i")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -1851,19 +2327,20 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.58.0") + (version "2.60.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) + "0ai0fg0w4l0a7avbafdbqjgjpg91myxalwrg2i3ixm1l2lyyfyah")))) (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))) @@ -1875,17 +2352,90 @@ matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.") (license license:artistic2.0))) +(define-public r-biovizbase + (package + (name "r-biovizbase") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biovizBase" version)) + (sha256 + (base32 + "14jyyg3ggdhaqhp0j4qf6dapykh76fygbaa4lr7czqbc5mr0iw23")))) + (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))) + (home-page "https://bioconductor.org/packages/biovizBase") + (synopsis "Basic graphic utilities for visualization of genomic data") + (description + "The biovizBase package is designed to provide a set of utilities, color +schemes and conventions for genomic data. It serves as the base for various +high-level packages for biological data visualization. This saves development +effort and encourages consistency.") + (license license:artistic2.0))) + +(define-public r-bsgenome + (package + (name "r-bsgenome") + (version "1.60.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome" version)) + (sha256 + (base32 + "1jhissp9ad1rn2p0bzr3yslbn84yqbaqgnn5p9hyacwr7mr091cn")))) + (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))) + (home-page "https://bioconductor.org/packages/BSgenome") + (synopsis "Infrastructure for Biostrings-based genome data packages") + (description + "This package provides infrastructure shared by all Biostrings-based +genome data packages and support for efficient SNP representation.") + (license license:artistic2.0))) + (define-public r-category (package (name "r-category") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr")))) + "0f76pb7h8qc51mca5pq00m9p02sbkcj6ywfzli20qai2ykpfr71x")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -1906,17 +2456,201 @@ biological sequences or sets of sequences.") analysis.") (license license:artistic2.0))) +(define-public r-chipseeker + (package + (name "r-chipseeker") + (version "1.28.3") + (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))) + (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 +genes around the peak, annotate genomic region of the peak, statstical methods +for estimate the significance of overlap among ChIP peak data sets, and +incorporate GEO database for user to compare the own dataset with those +deposited in database. The comparison can be used to infer cooperative +regulation and thus can be used to generate hypotheses. Several visualization +functions are implemented to summarize the coverage of the peak experiment, +average profile and heatmap of peaks binding to TSS regions, genomic +annotation, distance to TSS, and overlap of peaks or genes.") + (license license:artistic2.0))) + +(define-public r-chipseq + (package + (name "r-chipseq") + (version "1.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "chipseq" version)) + (sha256 + (base32 + "078p9h0zghlhpd6cr54nww1mk7q97imx8yqfayw5m2yq4097ivbi")))) + (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))) + (home-page "https://bioconductor.org/packages/chipseq") + (synopsis "Package for analyzing ChIPseq data") + (description + "This package provides tools for processing short read data from ChIPseq +experiments.") + (license license:artistic2.0))) + +(define-public r-complexheatmap + (package + (name "r-complexheatmap") + (version "2.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ComplexHeatmap" version)) + (sha256 + (base32 + "0jl96msj1njdrvngg68s50vmphvhi2lfwlv34x07pcdzgkjjs41f")))) + (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))) + (home-page + "https://github.com/jokergoo/ComplexHeatmap") + (synopsis "Making Complex Heatmaps") + (description + "Complex heatmaps are efficient to visualize associations between +different sources of data sets and reveal potential structures. This package +provides a highly flexible way to arrange multiple heatmaps and supports +self-defined annotation graphics.") + (license license:gpl2+))) + +(define-public r-copywriter + (package + (name "r-copywriter") + (version "2.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CopywriteR" version)) + (sha256 + (base32 + "0pacs714d9b1fdz68pp9ca0x77d376s19lxb82np4l9fgx0rgkxp")))) + (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))) + (home-page "https://github.com/PeeperLab/CopywriteR") + (synopsis "Copy number information from targeted sequencing") + (description + "CopywriteR extracts DNA copy number information from targeted sequencing +by utilizing off-target reads. It allows for extracting uniformly distributed +copy number information, can be used without reference, and can be applied to +sequencing data obtained from various techniques including chromatin +immunoprecipitation and target enrichment on small gene panels. Thereby, +CopywriteR constitutes a widely applicable alternative to available copy +number detection tools.") + (license license:gpl2))) + +(define-public r-deseq + (package + (name "r-deseq") + (version "1.39.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DESeq" version)) + (sha256 + (base32 + "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) + (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))) + (home-page "https://www-huber.embl.de/users/anders/DESeq/") + (synopsis "Differential gene expression analysis") + (description + "This package provides tools for estimating variance-mean dependence in +count data from high-throughput genetic sequencing assays and for testing for +differential expression based on a model using the negative binomial +distribution.") + (license license:gpl3+))) + (define-public r-deseq2 (package (name "r-deseq2") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1i0jpzsm1vl7q6qdmplj45w13lsaycxrx5pazlanjba2khn79k19")))) + "0r1brwmj7av0bj72jajn27vx3zs1bgg8qfbhf02fln6kf7im4kaz")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -1947,14 +2681,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi")))) + "1zywh30f4j4rj0f9w6yk5xr9mvdbg8gicy3wsb8yxdnamadyr7x4")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -1989,16 +2723,85 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-dirichletmultinomial + (package + (name "r-dirichletmultinomial") + (version "1.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DirichletMultinomial" version)) + (sha256 + (base32 + "0ikmj0300lfzj6q1vyahfyx5kwi5h59mds7ym4f2j1bbxqzy6ssl")))) + (properties + `((upstream-name . "DirichletMultinomial"))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/DirichletMultinomial") + (synopsis "Dirichlet-Multinomial mixture models for microbiome data") + (description + "Dirichlet-multinomial mixture models can be used to describe variability +in microbial metagenomic data. This package is an interface to code +originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): +1-15.") + (license license:lgpl3))) + +(define-public r-edaseq + (package + (name "r-edaseq") + (version "2.26.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EDASeq" version)) + (sha256 + (base32 + "0pakcbkalhhqz3d9lpfx3hscf53k24mlmrywxxzfg43yq57srkql")))) + (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))) + (home-page "https://github.com/drisso/EDASeq") + (synopsis "Exploratory data analysis and normalization for RNA-Seq") + (description + "This package provides support for numerical and graphical summaries of +RNA-Seq genomic read data. Provided within-lane normalization procedures to +adjust for GC-content effect (or other gene-level effects) on read counts: +loess robust local regression, global-scaling, and full-quantile +normalization. Between-lane normalization procedures to adjust for +distributional differences between lanes (e.g., sequencing depth): +global-scaling and full-quantile normalization.") + (license license:artistic2.0))) + (define-public r-edger (package (name "r-edger") - (version "3.32.1") + (version "3.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) + "0f6apsjq6cn794840ls9y2n0hix1gyhvkdgxch1v22qr4sq0c86k")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -2017,17 +2820,123 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.") (license license:gpl2+))) +(define-public r-ensembldb + (package + (name "r-ensembldb") + (version "2.16.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ensembldb" version)) + (sha256 + (base32 + "15yllkxr6sj5pfvkvv285nk3q5374nzq1iz8ywmnrq910k3xagd8")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jotsetung/ensembldb") + (synopsis "Utilities to create and use Ensembl-based annotation databases") + (description + "The package provides functions to create and use transcript-centric +annotation databases/packages. The annotation for the databases are directly +fetched from Ensembl using their Perl API. The functionality and data is +similar to that of the TxDb packages from the @code{GenomicFeatures} package, +but, in addition to retrieve all gene/transcript models and annotations from +the database, the @code{ensembldb} package also provides a filter framework +allowing to retrieve annotations for specific entries like genes encoded on a +chromosome region or transcript models of lincRNA genes.") + ;; No version specified + (license license:lgpl3+))) + +(define-public r-fastseg + (package + (name "r-fastseg") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "fastseg" version)) + (sha256 + (base32 + "006v7qs707xmnr35b7rw135pyvacrmhv55a3c53birkpsrjgkps0")))) + (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))) + (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") + (synopsis "Fast segmentation algorithm for genetic sequencing data") + (description + "Fastseg implements a very fast and efficient segmentation algorithm. +It can segment data from DNA microarrays and data from next generation +sequencing for example to detect copy number segments. Further it can segment +data from RNA microarrays like tiling arrays to identify transcripts. Most +generally, it can segment data given as a matrix or as a vector. Various data +formats can be used as input to fastseg like expression set objects for +microarrays or GRanges for sequencing data.") + (license license:lgpl2.0+))) + +(define-public r-gage + (package + (name "r-gage") + (version "2.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gage" version)) + (sha256 + (base32 + "0z7hrwdm6my6p7z04bcpfhqk72pd0s1bdzvsiiym59qj79fbvb83")))) + (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))) + (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" + "articles/10.1186/1471-2105-10-161")) + (synopsis "Generally applicable gene-set enrichment for pathway analysis") + (description + "GAGE is a published method for gene set (enrichment or GSEA) or pathway +analysis. GAGE is generally applicable independent of microarray or RNA-Seq +data attributes including sample sizes, experimental designs, assay platforms, +and other types of heterogeneity. The gage package provides functions for +basic GAGE analysis, result processing and presentation. In addition, it +provides demo microarray data and commonly used gene set data based on KEGG +pathways and GO terms. These functions and data are also useful for gene set +analysis using other methods.") + (license license:gpl2+))) + (define-public r-genefilter (package (name "r-genefilter") - (version "1.72.1") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn")))) + "0dy9pmlb0pc9b4ks5fb9zgnmhc9f2mkqmsdlb7f5z88xmj68y4qk")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) @@ -2045,16 +2954,83 @@ CAGE.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-geneoverlap + (package + (name "r-geneoverlap") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GeneOverlap" version)) + (sha256 + (base32 + "1kfw3h68rvbafhklds6sfmviwv91nms8wk0ywzkjg5h3mmgxbsv9")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-gplots" ,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 +and visualize the results.") + (license license:gpl3))) + +(define-public r-genomation + (package + (name "r-genomation") + (version "1.24.0") + (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))) + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") + (synopsis "Summary, annotation and visualization of genomic data") + (description + "This package provides a package for summary and annotation of genomic +intervals. Users can visualize and quantify genomic intervals over +pre-defined functional regions, such as promoters, exons, introns, etc. The +genomic intervals represent regions with a defined chromosome position, which +may be associated with a score, such as aligned reads from HT-seq experiments, +TF binding sites, methylation scores, etc. The package can use any tabular +genomic feature data as long as it has minimal information on the locations of +genomic intervals. In addition, it can use BAM or BigWig files as input.") + (license license:artistic2.0))) + (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.26.6") + (version "1.28.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1wy4dwiv0pgim975var802z565py4a0nakx6zdvbhry4c0dfczd1")))) + "0fjpgvpvyvl8cqgh2annib6h0c5li3aqz1ajfh5z5k5d0avdm4w0")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -2075,16 +3051,127 @@ translation between different chromosome sequence naming conventions (e.g., names in their natural, rather than lexicographic, order.") (license license:artistic2.0))) +(define-public r-genomicalignments + (package + (name "r-genomicalignments") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicAlignments" version)) + (sha256 + (base32 + "00rq110jkh89nxgk05zh8kssxk8mb4dq0wjg3n7ivfmmm9wdwhp2")))) + (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))) + (home-page "https://bioconductor.org/packages/GenomicAlignments") + (synopsis "Representation and manipulation of short genomic alignments") + (description + "This package provides efficient containers for storing and manipulating +short genomic alignments (typically obtained by aligning short reads to a +reference genome). This includes read counting, computing the coverage, +junction detection, and working with the nucleotide content of the +alignments.") + (license license:artistic2.0))) + +(define-public r-genomicfeatures + (package + (name "r-genomicfeatures") + (version "1.44.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFeatures" version)) + (sha256 + (base32 + "091p8xnf2xkqhind81vyv1rmy2fz2b3qalcbrsw4qnp24vgdv2am")))) + (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))) + (home-page "https://bioconductor.org/packages/GenomicFeatures") + (synopsis "Tools for working with transcript centric annotations") + (description + "This package provides a set of tools and methods for making and +manipulating transcript centric annotations. With these tools the user can +easily download the genomic locations of the transcripts, exons and cds of a +given organism, from either the UCSC Genome Browser or a BioMart +database (more sources will be supported in the future). This information is +then stored in a local database that keeps track of the relationship between +transcripts, exons, cds and genes. Flexible methods are provided for +extracting the desired features in a convenient format.") + (license license:artistic2.0))) + +(define-public r-genomicfiles + (package + (name "r-genomicfiles") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFiles" version)) + (sha256 + (base32 + "1plh14m7w6calw5yxcxp7g4bg8q00ax85m517wap78bni975k13y")))) + (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))) + (home-page "https://bioconductor.org/packages/GenomicFiles") + (synopsis "Distributed computing by file or by range") + (description + "This package provides infrastructure for parallel computations +distributed by file or by range. User defined mapper and reducer functions +provide added flexibility for data combination and manipulation.") + (license license:artistic2.0))) + (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) + "1qxc6dcwdlkan3hg0j9yfhz7gyi9qg671yj6zizsk6mzl7qqva0x")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -2109,14 +3196,14 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-gostats (package (name "r-gostats") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j")))) + "0jjswy6qmfgr2f6vk3y9pdvs9x91gn31h55qllgh0qb2cb26g9wa")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -2140,14 +3227,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.52.1") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i")))) + "0946kkykms79mqnx262q20xzrrhv7cv723xh378335ff41qyf63n")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -2169,14 +3256,14 @@ Enrichment Analysis} (GSEA).") (define-public r-hpar (package (name "r-hpar") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr")))) + "0q5pp04rq2gsh1kibvp8bvjkqc1kb46qpnj6agqp2vyqhrrfrm99")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -2186,16 +3273,120 @@ Enrichment Analysis} (GSEA).") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-rhtslib + (package + (name "r-rhtslib") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rhtslib" version)) + (sha256 + (base32 + "0acpgv98529ic2i2k03knz05akb6h51wbz7sr5zgi8gk4nmawrlf")))) + (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))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/nhayden/Rhtslib") + (synopsis "High-throughput sequencing library as an R package") + (description + "This package provides the HTSlib C library for high-throughput +nucleotide sequence analysis. The package is primarily useful to developers +of other R packages who wish to make use of HTSlib.") + (license license:lgpl2.0+))) + +(define-public r-impute + (package + (name "r-impute") + (version "1.66.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "impute" version)) + (sha256 + (base32 + "0pprkv25avxhllddcssvqvy3nibmqkfwaq4xnlhka7858gyiyd1k")))) + (native-inputs + `(("gfortran" ,gfortran))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/impute") + (synopsis "Imputation for microarray data") + (description + "This package provides a function to impute missing gene expression +microarray data, using nearest neighbor averaging.") + (license license:gpl2+))) + +(define-public r-interactivedisplaybase + (package + (name "r-interactivedisplaybase") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "interactiveDisplayBase" version)) + (sha256 + (base32 + "00rgrrmglslgb6j7whp0m5dlyl4436r647br05rrpv8cxrmbs2iv")))) + (properties + `((upstream-name . "interactiveDisplayBase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-dt" ,r-dt) + ("r-shiny" ,r-shiny))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/interactiveDisplayBase") + (synopsis "Base package for web displays of Bioconductor objects") + (description + "This package contains the basic methods needed to generate interactive +Shiny-based display methods for Bioconductor objects.") + (license license:artistic2.0))) + +(define-public r-keggrest + (package + (name "r-keggrest") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "KEGGREST" version)) + (sha256 + (base32 + "15313d20v3ziyn52fhc6fbzcy1kxjkdx18124bxhdfd14f4aypcd")))) + (properties `((upstream-name . "KEGGREST"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-httr" ,r-httr) + ("r-png" ,r-png))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/KEGGREST") + (synopsis "Client-side REST access to KEGG") + (description + "This package provides a package that provides a client interface to the +@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") + (license license:artistic2.0))) + (define-public r-limma (package (name "r-limma") - (version "3.46.0") + (version "3.48.3") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz")))) + "0385ac0hvvml99krcgcpp6q7layjhzgp9xcxkcjrpfg5mjg1z4sx")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -2205,17 +3396,408 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-methylkit + (package + (name "r-methylkit") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "methylKit" version)) + (sha256 + (base32 + "147nag4rz2xpjkkf8rmhja9k4ixjj1hsb0lq3lw7mw6q67zxsvf3")))) + (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 + (home-page "https://github.com/al2na/methylKit") + (synopsis + "DNA methylation analysis from high-throughput bisulfite sequencing results") + (description + "MethylKit is an R package for DNA methylation analysis and annotation +from high-throughput bisulfite sequencing. The package is designed to deal +with sequencing data from @dfn{Reduced representation bisulfite +sequencing} (RRBS) and its variants, but also target-capture methods and whole +genome bisulfite sequencing. It also has functions to analyze base-pair +resolution 5hmC data from experimental protocols such as oxBS-Seq and +TAB-Seq.") + (license license:artistic2.0))) + +(define-public r-motifrg + (package + (name "r-motifrg") + (version "1.31.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "motifRG" version)) + (sha256 + (base32 + "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn")))) + (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))) + (home-page "https://bioconductor.org/packages/motifRG") + (synopsis "Discover motifs in high throughput sequencing data") + (description + "This package provides tools for discriminative motif discovery in high +throughput genetic sequencing data sets using regression methods.") + (license license:artistic2.0))) + +(define-public r-mutationalpatterns + (package + (name "r-mutationalpatterns") + (version "3.2.0") + (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))) + (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 +characterization and visualization of a wide range of mutational patterns +in SNV base substitution data.") + (license license:expat))) + +(define-public r-msnbase + (package + (name "r-msnbase") + (version "2.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MSnbase" version)) + (sha256 + (base32 + "1z7s17j6zgb70m0khyf9icqlnbnzlivca7vw7j0vxyw417ld9lkr")))) + (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))) + (home-page "https://github.com/lgatto/MSnbase") + (synopsis "Base functions and classes for MS-based proteomics") + (description + "This package provides basic plotting, data manipulation and processing +of mass spectrometry based proteomics data.") + (license license:artistic2.0))) + +(define-public r-msnid + (package + (name "r-msnid") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MSnID" version)) + (sha256 + (base32 + "0r3vgigf4fk0xzfg8gcvad01jdh0fysh6x22m9qy77x6glyrxcj2")))) + (properties `((upstream-name . "MSnID"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (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))) + (home-page "https://bioconductor.org/packages/MSnID") + (synopsis "Utilities for LC-MSn proteomics identifications") + (description + "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data +from mzIdentML (leveraging the mzID package) or text files. After collating +the search results from multiple datasets it assesses their identification +quality and optimize filtering criteria to achieve the maximum number of +identifications while not exceeding a specified false discovery rate. It also +contains a number of utilities to explore the MS/MS results and assess missed +and irregular enzymatic cleavages, mass measurement accuracy, etc.") + (license license:artistic2.0))) + +(define-public r-mzid + (package + (name "r-mzid") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mzID" version)) + (sha256 + (base32 + "1wsy6frxa5602jqb1nlqv39mzgpid8wfyvb9m2jb6srv7p59rgys")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/mzID") + (synopsis "Parser for mzIdentML files") + (description + "This package provides a parser for mzIdentML files implemented using the +XML package. The parser tries to be general and able to handle all types of +mzIdentML files with the drawback of having less pretty output than a vendor +specific parser.") + (license license:gpl2+))) + +(define-public r-mzr + (package + (name "r-mzr") + (version "2.26.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mzR" version)) + (sha256 + (base32 + "0z4cz6lir9gwzy0hxwv03wv36fkkfdb97p9wv4af020k0zkp3ipr")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/boost") + #t)))) + (properties `((upstream-name . "mzR"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-boost + (lambda _ + (substitute* "src/Makevars" + (("\\./boost/libs.*") "") + (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") + (("\\ARCH_OBJS=" line) + (string-append line + "\nBOOST_LIBS=-lboost_system -lboost_regex \ +-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))) + (home-page "https://github.com/sneumann/mzR/") + (synopsis "Parser for mass spectrometry data files") + (description + "The mzR package provides a unified API to the common file formats and +parsers available for mass spectrometry data. It comes with a wrapper for the +ISB random access parser for mass spectrometry mzXML, mzData and mzML files. +The package contains the original code written by the ISB, and a subset of the +proteowizard library for mzML and mzIdentML. The netCDF reading code has +previously been used in XCMS.") + (license license:artistic2.0))) + +(define-public r-organismdbi + (package + (name "r-organismdbi") + (version "1.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "OrganismDbi" version)) + (sha256 + (base32 + "0p8ccpdchdwci4kv9y07wdadzgms8nipvg6rm1rll35jcflnnkxi")))) + (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))) + (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 +annotation packages each of which has its own schema by taking advantage of +the fact that each of these packages implements a select methods.") + (license license:artistic2.0))) + +(define-public r-pcamethods + (package + (name "r-pcamethods") + (version "1.84.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pcaMethods" version)) + (sha256 + (base32 + "1ccqsxn487dy92c2d1iffh9917z4zq5ia92zv2h6pi00jjc6ymb5")))) + (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))) + (home-page "https://github.com/hredestig/pcamethods") + (synopsis "Collection of PCA methods") + (description + "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, +Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method +for missing value estimation is included for comparison. BPCA, PPCA and +NipalsPCA may be used to perform PCA on incomplete data as well as for +accurate missing value estimation. A set of methods for printing and plotting +the results is also provided. All PCA methods make use of the same data +structure (pcaRes) to provide a common interface to the PCA results.") + (license license:gpl3+))) + +(define-public r-protgenerics + (package + (name "r-protgenerics") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ProtGenerics" version)) + (sha256 + (base32 + "1c79k8nc28782w5gxi7pkm8jmddq1hdw6khs9kgsp8dyk60ak6fq")))) + (properties `((upstream-name . "ProtGenerics"))) + (build-system r-build-system) + (home-page "https://github.com/lgatto/ProtGenerics") + (synopsis "S4 generic functions for proteomics infrastructure") + (description + "This package provides S4 generic functions needed by Bioconductor +proteomics packages.") + (license license:artistic2.0))) + (define-public r-rbgl (package (name "r-rbgl") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz")))) + "0l40ibf8g5s4ay83s92l198jjqc5l09hcmxqcjrpifvp5pjf9yy5")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs @@ -2228,17 +3810,67 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") the graph algorithms contained in the Boost library.") (license license:artistic2.0))) +(define-public r-rcas + (package + (name "r-rcas") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "RCAS" version)) + (sha256 + (base32 + "0l92v870ndna8zjqwzf22fb9vyhkh6942v4gaiqr1yc4qr521p5p")))) + (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))) + (synopsis "RNA-centric annotation system") + (description + "RCAS aims to be a standalone RNA-centric annotation system that provides +intuitive reports and publication-ready graphics. This package provides the R +library implementing most of the pipeline's features.") + (home-page "https://github.com/BIMSBbioinfo/RCAS") + (license license:artistic2.0))) + (define-public r-regioner (package (name "r-regioner") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi")))) + "0xzzaz3cl6pyxfsg0d931v8k15wbd05s5mnsb7igxldc5qqg3nsl")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -2262,14 +3894,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.30.2") + (version "2.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "1vvra7l29s7lnq996nwlpzbkrbdkr3ivkgmfp4kndfykxsl9q4vb")))) + "0wq9y649dh1am6djzz0xlz42428xsgw2bdx1dknhdw2xbydmmx47")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -2309,16 +3941,70 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-rhdf5 + (package + (name "r-rhdf5") + (version "2.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rhdf5" version)) + (sha256 + (base32 + "1a5kw9ry9cr258al0x3q0ss5xn1ymscdypx51vzzgzamhy7dqakz")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rhdf5filters" ,r-rhdf5filters) + ("r-rhdf5lib" ,r-rhdf5lib))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/rhdf5") + (synopsis "HDF5 interface to R") + (description + "This R/Bioconductor package provides an interface between HDF5 and R. +HDF5's main features are the ability to store and access very large and/or +complex datasets and a wide variety of metadata on mass storage (disk) through +a completely portable file format. The rhdf5 package is thus suited for the +exchange of large and/or complex datasets between R and other software +package, and for letting R applications work on datasets that are larger than +the available RAM.") + (license license:artistic2.0))) + +(define-public r-rhdf5filters + (package + (name "r-rhdf5filters") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rhdf5filters" version)) + (sha256 + (base32 + "133v0s452acspi4dbf6gsa2xrr0qza86jdjjbpwhdv6zfd1djbgc")))) + (properties `((upstream-name . "rhdf5filters"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rhdf5lib" ,r-rhdf5lib))) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/grimbough/rhdf5filters") + (synopsis "HDF5 compression filters") + (description + "This package provides a collection of compression filters for use with +HDF5 datasets.") + (license license:bsd-2))) + (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) + "0arhh5bbx3pmxmkh5sjgczcswqy83d35r7cjhd2knpczdvrixaq5")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -2330,8 +4016,7 @@ browser.") (substitute* "DESCRIPTION" (("zlibbioc, ") "")) (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) + (("import\\(zlibbioc\\)") ""))))))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) @@ -2352,17 +4037,173 @@ Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.") (license license:expat))) +;; This is a CRAN package, but it depends on a Bioconductor package: +;; s4vectors. +(define-public r-restfulr + (package + (name "r-restfulr") + (version "0.0.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "restfulr" version)) + (sha256 + (base32 + "1dk45mzrr6ka92yjz7hfhkj12kpx1wg4szv1h1mg80mgga4ganbv")))) + (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))) + (home-page "https://cran.r-project.org/package=restfulr") + (synopsis "R interface to RESTful web services") + (description + "This package models a RESTful service as if it were a nested R list.") + (license license:artistic2.0))) + +(define-public r-rtracklayer + (package + (name "r-rtracklayer") + (version "1.52.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rtracklayer" version)) + (sha256 + (base32 + "11w6dx09pb49lin1gr9q88xn7ixh9jd5z6m9z27djchm0nw10lx9")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + ((" zlibbioc,") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") ""))))))) + (native-inputs + `(("pkg-config" ,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))) + (home-page "https://bioconductor.org/packages/rtracklayer") + (synopsis "R interface to genome browsers and their annotation tracks") + (description + "rtracklayer is an extensible framework for interacting with multiple +genome browsers (currently UCSC built-in) and manipulating annotation tracks +in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit +built-in). The user may export/import tracks to/from the supported browsers, +as well as query and modify the browser state, such as the current viewport.") + (license license:artistic2.0))) + +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-samr + (package + (name "r-samr") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "samr" version)) + (sha256 + (base32 + "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) + (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))) + (home-page "https://statweb.stanford.edu/~tibs/SAM/") + (synopsis "Significance analysis of Microarrays") + (description + "This is a package for significance analysis of Microarrays for +differential expression analysis, RNAseq data and related problems.") + ;; Any version of the LGPL + (license license:lgpl3+))) + +(define-public r-seqlogo + (package + (name "r-seqlogo") + (version "1.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "seqLogo" version)) + (sha256 + (base32 + "1253sj1hc6bbrff0iv5xa3v9znqvisll0fy6fdjka9c778fn4mcp")))) + (properties `((upstream-name . "seqLogo"))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/seqLogo") + (synopsis "Sequence logos for DNA sequence alignments") + (description + "seqLogo takes the position weight matrix of a DNA sequence motif and +plots the corresponding sequence logo as introduced by Schneider and +Stephens (1990).") + (license license:lgpl2.0+))) + +(define-public r-seqpattern + (package + (name "r-seqpattern") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "seqPattern" version)) + (sha256 + (base32 + "0h74z84zyvfzclsm0g13b95hirn99185wc6lp53jkzah9yyi59ay")))) + (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))) + (home-page "https://bioconductor.org/packages/seqPattern") + (synopsis "Visualising oligonucleotide patterns and motif occurrences") + (description + "This package provides tools to visualize oligonucleotide patterns and +sequence motif occurrences across a large set of sequences centred at a common +reference point and sorted by a user defined feature.") + (license license:gpl3+))) + (define-public r-shortread (package (name "r-shortread") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) + "0zqinw3c6h5v1c5nhzkiziirws16nbviccgw8nj2d22r33dbqwp3")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -2395,17 +4236,220 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-simplifyenrichment + (package + (name "r-simplifyenrichment") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "simplifyEnrichment" version)) + (sha256 + (base32 + "0rqa414kvyjjmj4932zk39rqa14z13b57rkrxdrf16jmq2r437vh")))) + (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))) + (home-page "https://github.com/jokergoo/simplifyEnrichment") + (synopsis "Simplify functional enrichment results") + (description "This package provides a new clustering algorithm, binary +cut, for clustering similarity matrices of functional terms is implemented in +this package. It also provides functionalities for visualizing, summarizing +and comparing the clusterings.") + (license license:expat))) + +(define-public r-trajectoryutils + (package + (name "r-trajectoryutils") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TrajectoryUtils" version)) + (sha256 + (base32 + "1b7mg3ypp1ay98cav47h9vn692lx0n9b5b0hpansgnkr5prb823b")))) + (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))) + (home-page "https://bioconductor.org/packages/TrajectoryUtils") + (synopsis "Single-cell trajectory analysis utilities") + (description + "This package implements low-level utilities for single-cell trajectory +analysis, primarily intended for re-use inside higher-level packages. It +includes a function to create a cluster-level minimum spanning tree and data +structures to hold pseudotime inference results.") + (license license:gpl3))) + +(define-public r-slingshot + (package + (name "r-slingshot") + (version "2.0.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "slingshot" version)) + (sha256 + (base32 + "1aqsz2kxwax8d8d5iv3zk5hlyk5aya1wbxs1wky2rgccw4d35whx")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/slingshot") + (synopsis "Tools for ordering single-cell sequencing") + (description "This package provides functions for inferring continuous, +branching lineage structures in low-dimensional data. Slingshot was designed +to model developmental trajectories in single-cell RNA sequencing data and +serve as a component in an analysis pipeline after dimensionality reduction +and clustering. It is flexible enough to handle arbitrarily many branching +events and allows for the incorporation of prior knowledge through supervised +graph construction.") + (license license:artistic2.0))) + +(define-public r-structuralvariantannotation + (package + (name "r-structuralvariantannotation") + (version "1.8.2") + (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))) + (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/") + (synopsis "R package designed to simplify structural variant analysis") + (description + "This package contains useful helper functions for dealing with structural +variants in VCF format. The packages contains functions for parsing VCFs from +a number of popular callers as well as functions for dealing with breakpoints +involving two separate genomic loci encoded as GRanges objects.") + (license license:gpl3))) + +(define-public r-summarizedexperiment + (package + (name "r-summarizedexperiment") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "SummarizedExperiment" version)) + (sha256 + (base32 + "16np5ik6jgbi68mhlib6yskywwbaa50mlr7m3sh1hqk889whfn1g")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/SummarizedExperiment") + (synopsis "Container for representing genomic ranges by sample") + (description + "The SummarizedExperiment container contains one or more assays, each +represented by a matrix-like object of numeric or other mode. The rows +typically represent genomic ranges of interest and the columns represent +samples.") + (license license:artistic2.0))) + +(define-public r-sva + (package + (name "r-sva") + (version "3.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "sva" version)) + (sha256 + (base32 + "12jkcybdfspabh7x124d44l9fj1hwwg3gvcqxvz5wpkiflc2vkji")))) + (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))) + (home-page "https://bioconductor.org/packages/sva") + (synopsis "Surrogate variable analysis") + (description + "This package contains functions for removing batch effects and other +unwanted variation in high-throughput experiment. It also contains functions +for identifying and building surrogate variables for high-dimensional data +sets. Surrogate variables are covariates constructed directly from +high-dimensional data like gene expression/RNA sequencing/methylation/brain +imaging data that can be used in subsequent analyses to adjust for unknown, +unmodeled, or latent sources of noise.") + (license license:artistic2.0))) + (define-public r-systempiper (package (name "r-systempiper") - (version "1.24.3") + (version "1.26.3") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki")))) + "01l35l5zj87qkarrbal9la6kshk3j7k8hy3iimv3gdnnz4axmvs7")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -2413,6 +4457,7 @@ ungapped alignment formats.") ("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) @@ -2428,9 +4473,11 @@ ungapped alignment formats.") ("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 @@ -2449,16 +4496,73 @@ experimental designs is facilitated by a consistently implemented sample annotation infrastructure.") (license license:artistic2.0))) +(define-public r-topgo + (package + (name "r-topgo") + (version "2.44.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "topGO" version)) + (sha256 + (base32 + "1ggi7yrhkyi85p3sfj3yd95n9mzq1xpff28ixa4dl9yzasks1v5a")))) + (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))) + (home-page "https://bioconductor.org/packages/topGO") + (synopsis "Enrichment analysis for gene ontology") + (description + "The topGO package provides tools for testing @dfn{gene ontology} (GO) +terms while accounting for the topology of the GO graph. Different test +statistics and different methods for eliminating local similarities and +dependencies between GO terms can be implemented and applied.") + ;; Any version of the LGPL applies. + (license license:lgpl2.1+))) + +(define-public r-tximport + (package + (name "r-tximport") + (version "1.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tximport" version)) + (sha256 + (base32 + "0ip2yr0zspf2aagskxl4dwncr48dw5qb90an3sswnnh2dqdb82if")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/tximport") + (synopsis "Import and summarize transcript-level estimates for gene-level analysis") + (description + "This package provides tools to import transcript-level abundance, +estimated counts and transcript lengths, and to summarize them into matrices +for use with downstream gene-level analysis packages. Average transcript +length, weighted by sample-specific transcript abundance estimates, is +provided as a matrix which can be used as an offset for different expression +of gene-level counts.") + (license license:gpl2+))) + (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) + "0c9r00j8a3bs6n0dv4wi17jc1ljzvr3r2bi4h9axhcsf2ip906rh")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs @@ -2487,16 +4591,52 @@ annotation infrastructure.") coding changes and predict coding outcomes.") (license license:artistic2.0))) +(define-public r-vsn + (package + (name "r-vsn") + (version "3.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "vsn" version)) + (sha256 + (base32 + "0nppph3kv8z83368snb8s3n4vcqj829yyi1kh4q09qvq18rhvssv")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") + (synopsis "Variance stabilization and calibration for microarray data") + (description + "The package implements a method for normalising microarray intensities, +and works for single- and multiple-color arrays. It can also be used for data +from other technologies, as long as they have similar format. The method uses +a robust variant of the maximum-likelihood estimator for an +additive-multiplicative error model and affine calibration. The model +incorporates data calibration step (a.k.a. normalization), a model for the +dependence of the variance on the mean intensity and a variance stabilizing +data transformation. Differences between transformed intensities are +analogous to \"normalized log-ratios\". However, in contrast to the latter, +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-xvector (package (name "r-xvector") - (version "0.30.0") + (version "0.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) + "1cw34gd9iaspl0v737xl7rngq63zrj03a5ngai15ggrnv1sq2aqr")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -2523,17 +4663,36 @@ coding changes and predict coding outcomes.") \"externally\" (behind an R external pointer, or on disk).") (license license:artistic2.0))) +(define-public r-zlibbioc + (package + (name "r-zlibbioc") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "zlibbioc" version)) + (sha256 + (base32 + "1dv5bf12kzk1yzyfs3g5syim16sbi44kalvzj2i2xcnxnl6x60ip")))) + (properties + `((upstream-name . "zlibbioc"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/zlibbioc") + (synopsis "Provider for zlib-1.2.5 to R packages") + (description "This package uses the source code of zlib-1.2.5 to create +libraries for systems that do not have these available via other means.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx")))) + "1d085lfa3yif5wkys1fb0zzgg0cqwd1y18vasgqqdr6rva075d4z")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -2551,14 +4710,14 @@ coding changes and predict coding outcomes.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy")))) + "1nsfyfpj264h6y322pzz0i001b0m862j3skbq5rjwlrj1p8j2gi7")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -2586,14 +4745,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.54.1") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3")))) + "0fyq77im6s79havjwbchhqhnllxs134jsi98g6msxz66h16lj3al")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -2622,14 +4781,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5")))) + "0xssanffh1hr7f48mnazcpwi25rdp7mxlyb9nbf4q2mp7m40jnpm")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -2677,13 +4836,13 @@ integration with @code{Rcpp}.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2")))) + "1xld6ar440achik4dbd7vhiw6jfj0sb96jm52n7hav5bv4gag3mh")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs @@ -2704,13 +4863,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6")))) + "1g9ja8p90czx83ar0l9ran7m6aggvszdbqm714fq7z4rxq9b4hs3")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs @@ -2731,14 +4890,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.0.15") + (version "3.2.7") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "06f613s8d9z51njyf839g22gwybx9zs5n6xghwr5j1ad2n4m6qwi")))) + "01jfxcj5c0088vvsi3pz8fs0ka6n12l2j8s1d0rpqwa1y0444x7z")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -2806,17 +4965,49 @@ package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.") (license license:gpl2))) +(define-public r-mbkmeans + (package + (name "r-mbkmeans") + (version "1.8.0") + (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))) + (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 +large datasets, including support for on-disk data representation.") + (license license:expat))) + (define-public r-multtest (package (name "r-multtest") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q")))) + "1wi15v4llgv11hpb2j9h4a35nrnawnmvbz5d5dvgy8lhqrlq8w9a")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) @@ -2847,13 +5038,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4")))) + "1i7s198d5kw4gk6nqqsd3vqaknj4493p822f2za8q95gv6x02rxa")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) @@ -2945,14 +5136,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.24.2") + (version "3.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0l417aygs89wf1j9fjpfjhahzskbpbgcrm8xpx3qm4s0307vfzkw")))) + "1iqzm7pifl9zrw3s06i6h85n1p01pd06vh1a93izyfhgybxn262d")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -2969,6 +5160,7 @@ determining dependencies between variables, code improvement suggestions.") ("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) @@ -2998,13 +5190,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.2.1") + (version "1.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb")))) + "1yir3rwhz5vf0pdn3fpvlc57c75k98gvv8gapajbvymz3lyghijv")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -3025,12 +5217,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray")))) + (base32 "0wpmrhqpyv27h1hn31hzz21r74r7yqx79ljv8i8gn6ix8lf5ca56")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) @@ -3044,12 +5236,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4")))) + (base32 "1p87k4vw981k97d9bckmprrfg55jwd91658rgxzjj8hnschf28a4")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -3064,12 +5256,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba")))) + (base32 "1zik04y2q0anzy85l0b4ryzkxpfx2fnmpwp5s7akyk1jfl2r8gw7")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -3087,12 +5279,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph")))) + (base32 "1p4544xlarkbgs9kybrrawq3v7qr6ix62nrc6l7dcksh2ka69yzf")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -3120,14 +5312,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215")))) + "0hyc0sl2nf18bz0jxbzim0v41zwh2rnnr7l3p6zkk9wnw5gn7bbc")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -3146,14 +5338,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7")))) + "1kfxjh1mynrgqsy2q6byf03cbymqc8w7l7672iyd0wj5qzlif4h5")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -3180,14 +5372,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg")))) + "1jmd8yrv7p7hn4gdibg3svmhqxjyrnfp7cgsqg8zv862lgd75zsl")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -3221,14 +5413,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr")))) + "1m5w2j35wr0lzwir4s58z757vrcsj5mglsqrkvs241k0hlmn06qa")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -3247,16 +5439,16 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (license license:gpl3))) (define-public r-interactionset - (package ;BROKEN + (package (name "r-interactionset") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31")))) + "034xidjmn67n1471fnpdmz7gjm6p05cj8sp9nssc3gxdzn54a6xb")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -3283,14 +5475,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd")))) + "0zjl7rp5fk14kqsx0bkbpq6hqahbkiyvwa9aggp4kfb8hnmz9qal")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -3324,14 +5516,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp")))) + "1v8aysvy6a3r1iafc3xvk885c128kb3pb9zpcdhdjcn0by96k8hh")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") @@ -3344,14 +5536,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509")))) + "07qrxssx4rb8r958r1smx8xfpzdxpp55hci3201hcmz3mxz77i0s")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -3370,14 +5562,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv")))) + "0dsk8qmwimzmd1x4k4jwg9q11jm1ahn8cw0gzd6s2gmigfls4hsa")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs @@ -3403,14 +5595,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n")))) + "18wyi73l95df182vg3m014sxwdbpggr61vsbazhyw4vyx2fnzmpl")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -3427,14 +5619,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a")))) + "1rz5jk5bgpk7gjknx79jyslahjg46q2f4bx6dgd0vwmarc29a45z")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -3452,14 +5644,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483")))) + "0jh5db9dv5pb6b50sg22x8q55m3h0h0nkmb9mivvvp22dhyrd82z")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -3499,14 +5691,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg")))) + "1wiqmzjcb7flp7ldcgbx91asxxrmm1rg9pcfljniab9xcsldhksp")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs @@ -3528,14 +5720,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh")))) + "1fy0k1p0m209lzjpd5jhfnifa22lrn63qq3a3kn5g0xhbbmijzac")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -3556,14 +5748,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.8.2") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7")))) + "0cjidi18wjip9xzx83890wjk40vvjq06prf1ag4m2kac47w01r7v")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -3585,17 +5777,143 @@ to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.") (license license:gpl3))) +(define-public r-scaledmatrix + (package + (name "r-scaledmatrix") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ScaledMatrix" version)) + (sha256 + (base32 + "1j96fvw1waqxbv5c8myfmhsidq370z03yz13yqmrs4nn1rpn1a06")))) + (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))) + (home-page "https://github.com/LTLA/ScaledMatrix") + (synopsis "Create a DelayedMatrix of scaled and centered values") + (description + "This package provides delayed computation of a matrix of scaled and +centered values. The result is equivalent to using the @code{scale} function +but avoids explicit realization of a dense matrix during block processing. +This permits greater efficiency in common operations, most notably matrix +multiplication.") + (license license:gpl3))) + +(define-public r-treeio + (package + (name "r-treeio") + (version "1.16.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "treeio" version)) + (sha256 + (base32 + "1y60yvg1rl21cab9xrkns0209pg44mwr90qj099dvk97wsjkx67g")))) + (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))) + (home-page "https://github.com/YuLab-SMU/treeio") + (synopsis "Base classes and functions for Phylogenetic tree input and output") + (description + "This is an R package to make it easier to import and store phylogenetic +trees with associated data; and to link external data from different sources +to phylogeny. It also supports exporting phylogenetic trees with +heterogeneous associated data to a single tree file and can be served as a +platform for merging tree with associated data and converting file formats.") + (license license:artistic2.0))) + +(define-public r-ggtree + (package + (name "r-ggtree") + (version "3.0.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ggtree" version)) + (sha256 + (base32 + "0xf4b9vfdyzzivwgw4ymapl5bb4k9p04mmr53822kxgfd5qrs1zx")))) + (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))) + (home-page "https://yulab-smu.top/treedata-book/") + (synopsis "R package for visualization of trees and annotation data") + (description + "This package extends the ggplot2 plotting system which implements a +grammar of graphics. ggtree is designed for visualization and annotation of +phylogenetic trees and other tree-like structures with their annotation +data.") + (license license:artistic2.0))) + +(define-public r-metapod + (package + (name "r-metapod") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "metapod" version)) + (sha256 + (base32 + "1hbcwr6d8gyrf4azh0gi588xkrg6gz7gsb5hbvzqkhplbsp6shlv")))) + (properties `((upstream-name . "metapod"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/metapod") + (synopsis "Meta-analyses on p-values of differential analyses") + (description + "This package implements a variety of methods for combining p-values in +differential analyses of genome-scale datasets. Functions can combine +p-values across different tests in the same analysis (e.g., genomic windows in +ChIP-seq, exons in RNA-seq) or for corresponding tests across separate +analyses (e.g., replicated comparisons, effect of different treatment +conditions). Support is provided for handling log-transformed input p-values, +missing values and weighting where appropriate.") + (license license:gpl3))) + (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.6.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni")))) + "16gkwq8fb8jdchpnlzq2hz3i74a6pzbnc1bf93282h11mp7qr58l")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -3607,7 +5925,8 @@ achieved for all methods using the BiocParallel framework.") ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rsvd" ,r-rsvd) - ("r-s4vectors" ,r-s4vectors))) + ("r-s4vectors" ,r-s4vectors) + ("r-scaledmatrix" ,r-scaledmatrix))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/LTLA/BiocSingular") @@ -3666,14 +5985,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic")))) + "1ynp334hm76zf05j4f6vha6r16s5f2ncxx9yviq4rxidk9r723jq")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs @@ -3692,14 +6011,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag")))) + "0fbrf5s6pz115djm7xw95k1d0p7svi40aacbb3d52wmx5azwj424")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -3732,13 +6051,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm")))) + "03pvjzjrcsbjfw3855s3whfzin45vaipy7cahnj6fywdysvh8hps")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) @@ -3755,14 +6074,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc")))) + "0mgq814f6c2271d2lxg763bsnv3ma4ari5xa4x1rbksv8yvcjc4d")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -3855,14 +6174,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny")))) + "0h5v3vrb90zim80bdnr3aw58g3h7zjqa4l9i0jwx5j19ywf54fdz")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs @@ -3879,13 +6198,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2")))) + "11sgxz2xz685pgm8mf0hzm6aryx4fj5g3dlffjzpqxh3awfqa19p")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -3917,14 +6236,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9")))) + "0aw4b3p5z8ys7zlwy8s3bsqk03xwx42311yxr7q14w3f7sn3shzn")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -3947,14 +6266,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0")))) + "0b393a8ayzbnrgkk562w1dj7avacpb3wc7yq7awiki24wi5g2lfw")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs @@ -3979,14 +6298,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s")))) + "190rkx3sivj68in36hhin5v535yd6fvlvm7l90w1bl38zpb7p6jn")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -4012,17 +6331,91 @@ classification (assignment) methods. It also contains a Shiny application for interactive exploration of results.") (license license:gpl2+))) +(define-public r-residualmatrix + (package + (name "r-residualmatrix") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ResidualMatrix" version)) + (sha256 + (base32 + "0p7va19aw0j6anx7ck879kbi5cn7dy712h5ia94adr38ssismv1v")))) + (properties + `((upstream-name . "ResidualMatrix"))) + (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))) + (home-page "https://github.com/LTLA/ResidualMatrix") + (synopsis "Create a DelayedMatrix of regression residuals") + (description + "This package implements tools for delayed computation of a matrix of +residuals after fitting a linear model to each column of an input matrix. It +also supports partial computation of residuals where selected factors are to +be preserved in the output matrix. It implements a number of efficient +methods for operating on the delayed matrix of residuals, most notably matrix +multiplication and calculation of row/column sums or means.") + (license license:gpl3))) + +(define-public r-batchelor + (package + (name "r-batchelor") + (version "1.8.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "batchelor" version)) + (sha256 + (base32 + "1bkk69b5llkmvmpsnhymwjm2szmzypgszfsw8mak1b5ms5zf8lr0")))) + (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))) + (home-page "https://bioconductor.org/packages/batchelor") + (synopsis "Single-Cell Batch Correction Methods") + (description + "This package implements a variety of methods for batch correction of +single-cell (RNA sequencing) data. This includes methods based on detecting +mutually nearest neighbors, as well as several efficient variants of linear +regression of the log-expression values. Functions are also provided to +perform global rescaling to remove differences in depth between batches, and +to perform a principal components analysis that is robust to differences in +the numbers of cells across batches.") + (license license:gpl3))) + (define-public r-mast (package (name "r-mast") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn")))) + "1gkpagam5rap36viyr3n4psa658x9vckrxap1h67jasiiyrcfz2d")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs @@ -4050,14 +6443,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx")))) + "05j1vc51f39xalggdq27y7218gkr3zq7fh7jhzsb4jj7fpn837ry")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -4104,10 +6497,44 @@ tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.") (license license:artistic2.0))) +(define-public r-leidenbase + (let ((commit "430f22af6982cc7d2e6e77f6b0df47bc970dcbce") + (revision "1")) + (package + (name "r-leidenbase") + (version (git-version "0.1.3" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cole-trapnell-lab/leidenbase") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ylqsmdpv4xq6f6ldxvwkhk33a9i1jcgk60zvksk3iplykfzd6c0")))) + (properties `((upstream-name . "leidenbase"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("gfortran" ,gfortran))) + (propagated-inputs + `(("r-igraph" ,r-igraph))) + (home-page "https://github.com/cole-trapnell-lab/leidenbase") + (synopsis "R and C wrappers to run the Leiden find_partition function") + (description + "This package provides an R to C interface that runs the Leiden +community detection algorithm to find a basic partition. It runs the +equivalent of the @code{find_partition} function. This package includes the +required source code files from the official Leidenalg distribution and +several functions from the R igraph package.") + (license license:gpl3+)))) + (define-public r-monocle3 (package (name "r-monocle3") - (version "0.1.2") + (version "1.0.0") (source (origin (method git-fetch) @@ -4117,10 +6544,12 @@ qPCR data, but could be used with other types as well.") (file-name (git-file-name name version)) (sha256 (base32 - "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) + "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) + `(("r-assertthat" ,r-assertthat) + ("r-batchelor" ,r-batchelor) + ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dplyr" ,r-dplyr) @@ -4130,6 +6559,7 @@ qPCR data, but could be used with other types as well.") ("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) @@ -4149,6 +6579,7 @@ qPCR data, but could be used with other types as well.") ("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) @@ -4169,14 +6600,14 @@ qPCR data, but could be used with other types as well.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f")))) + "18d51dv2ygsm7kkwal341f1wrwrazyns0045j00vld367kic8jiz")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -4196,14 +6627,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g")))) + "1dw9m3m99apmbs32461c6lnmy81n5hxbhz3p8jk419gajkh4v1ji")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -4234,14 +6665,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.14.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73")))) + "0zw8g4mql7b02xqwhc1i0bnhm20c1q9xqc7yz84j98pqbi996vi5")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) @@ -4256,12 +6687,14 @@ distributions.") ("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))) @@ -4276,14 +6709,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4")))) + "0jhkdbcd03d5n8vn3xkad6f21xjkawyxc9rdwcj8vwc8alx730am")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs @@ -4309,14 +6742,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.32.0") + (version "0.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay")))) + "1sy0i3nbzsw4ymdxaiwpyx1vcg9yp3i8xfjcymqwhv95j3kyglv9")))) (build-system r-build-system) (propagated-inputs `(("r-base64" ,r-base64))) @@ -4330,14 +6763,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w")))) + "0lva0f255fcpy625frvij4n14q7nw4jcx8n2hlkxid4mgkfqwlhf")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -4356,14 +6789,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk")))) + "0wi38vwfi8qr10x4xifhylxx7vfc6fqvqs649iq7lf0y7islwq2v")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -4390,14 +6823,14 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi")))) + "189lzppvrz6bw2kpppawgsfjyh2ahyy8bi9z8srpas67qf2r8jmj")))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) @@ -4441,14 +6874,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh")))) + "1941rc524ssx8gwhmwk40mgfrhddfs6hgldvs7bi22r29gm4y7qj")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -4487,14 +6920,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3")))) + "0qjdxjdzfnnxcm07bf51v38388s5qf1i03l1sdb9jf3gxdh8yh02")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -4526,14 +6959,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3")))) + "035hrniycqadmkwg8rmzw8szv0amhy31390izy91rfrld31v2yy7")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -4587,14 +7020,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx")))) + "0fknlwdfd49v09zspg0337b0zzc8hqza3563yrw51viw3g35d6q3")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -4681,6 +7114,52 @@ Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and a routine for graphical display.") (license license:gpl2))) +(define-public r-tradeseq + (package + (name "r-tradeseq") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tradeSeq" version)) + (sha256 + (base32 + "0fgmb309pvqf3chdhqgbd4lzhahcj5g71sica33nzn98qhipldx7")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://statomics.github.io/tradeSeq/index.html") + (synopsis "Trajectory-based differential expression analysis") + (description + "This package provides a flexible method for fitting regression models that +can be used to find genes that are differentially expressed along one or +multiple lineages in a trajectory. Based on the fitted models, it uses a +variety of tests suited to answer different questions of interest, e.g. the +discovery of genes for which expression is associated with pseudotime, or which +are differentially expressed (in a specific region) along the trajectory. It +fits a negative binomial generalized additive model (GAM) for each gene, and +performs inference on the parameters of the GAM.") + (license license:expat))) + (define-public r-triform (package (name "r-triform") @@ -4708,14 +7187,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89")))) + "1gpzrln2clfrja8rzxhsis6bi1xqglh3h2lhvqlnrx4lqxhbkv9c")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -4748,14 +7227,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "2.36.0") + (version "3.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n")))) + "0xwg3sxmihg3p6v3nxgrqy0nrqxi6razg3b3rjh2gcb2vv8gcqng")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -4773,14 +7252,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.16.1") + (version "2.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs")))) + "00dbgkiv9x7g2i0anzcxpycwqqqry0y7jl3ad93lhvi31qnqq1sm")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -4802,14 +7281,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x")))) + "039bmcv5l44gszb6xapbihp3mfqdaaa8mfc05y702p78i7x93g5y")))) (build-system r-build-system) (propagated-inputs `(("r-multtest" ,r-multtest) @@ -4833,14 +7312,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l")))) + "1xz5nbw5dzyah8az7mpwj8m27fsvpi2jjhfg3n27dsv8rvdncqi8")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -4855,14 +7334,14 @@ phenotype of interest.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n")))) + "1mhdgy46nxgv7v54bk9bqfy0vgjzl1law7zy718swdd762xn6g9d")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -4887,14 +7366,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.16.0") + (version "3.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4")))) + "0kp6j42mpxrpd02cjrzqmrx3rvvpi90xiy4gc5km6ny3vxbhlaqw")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -4922,20 +7401,21 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.10.2") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv")))) + "194sfmcnjfi3fvvfpljg1f80f44vvvxiij336b8z1dgzki6bqa3r")))) (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) @@ -4958,14 +7438,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "3.18.1") + (version "4.0.5") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si")))) + "1dccrl2ffhgmv3iqlmpln7z86ahpf0j9ma194fnknsgi3cd9rhrl")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -4981,8 +7461,8 @@ All the visualization methods are developed based on ggplot2 graphics.") ("r-plyr" ,r-plyr) ("r-qvalue" ,r-qvalue) ("r-rlang" ,r-rlang) - ("r-rvcheck" ,r-rvcheck) - ("r-tidyr" ,r-tidyr))) + ("r-tidyr" ,r-tidyr) + ("r-yulab-utils" ,r-yulab-utils))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") @@ -4992,17 +7472,63 @@ All the visualization methods are developed based on ggplot2 graphics.") profiles (GO and KEGG) of gene and gene clusters.") (license license:artistic2.0))) +(define-public r-clusterexperiment + (package + (name "r-clusterexperiment") + (version "2.12.0") + (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))) + (home-page "https://bioconductor.org/packages/clusterExperiment/") + (synopsis "Compare clusterings for single-cell sequencing") + (description "This package provides functionality for running and comparing +many different clusterings of single-cell sequencing data or other large mRNA +expression data sets.") + (license license:artistic2.0))) + (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r")))) + "0ipzv7wdvfqhdyjiak956qq201igsdxm6dr6rh3dj6cssgsrnrpb")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -5016,6 +7542,7 @@ profiles (GO and KEGG) of gene and gene clusters.") ("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) @@ -5036,14 +7563,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.62.0") + (version "1.64.2") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i")))) + "03y633vgxprd2abhanj4sanmb4ymz7az5aiasxn6wjzawiqjdcb1")))) (build-system r-build-system) (arguments `(#:phases @@ -5051,11 +7578,11 @@ data in R and Bioconductor containers.") (add-after 'unpack 'remove-reference-to-non-free-data (lambda _ (substitute* "DESCRIPTION" - ((", KEGG.db") "")) - #t))))) + ((", 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))) (home-page "https://bioconductor.org/packages/annaffy/") @@ -5072,14 +7599,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2")))) + "00fi753nsayv0xspavw8r9ni1sim8ng33hp3d3kj2b8ihygd1s10")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -5097,14 +7624,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz")))) + "1lz85bys5dp5d1ir9c9c4wy85wkk62s14niyzzxaqrxpsji2p2iw")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -5127,14 +7654,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i")))) + "1jibm2f5glzsrvl64hxc5sf59d4w6ry0f663p619hfr44mi1mpri")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -5152,14 +7679,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy")))) + "09jjfby5znmg2fdkhpbinx2v21zrfa44qq7cylcn9ipffqx3pk86")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -5176,14 +7703,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp")))) + "101w4i0w8n7qhki22qr8l8wk8w6zalzmcywqm2g4238qv7xbnr8p")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -5207,14 +7734,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79")))) + "0bwn185admy5k99fkd2dhhvy7x1f75r0mqn5k24dbbg0paw6nnr8")))) (build-system r-build-system) (propagated-inputs `(("r-a4base" ,r-a4base) @@ -5232,14 +7759,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f")))) + "1xvk84gd1lfq1icrfwwd6y79zywrisfnc3knprigzzax31aks32c")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -5280,14 +7807,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47")))) + "1yp0675n1g8rxdjdd7w8al5c9jq96h0kfm8218mc50z0p2fasgbj")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) @@ -5307,14 +7834,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw")))) + "05drbhjqn5kik6k4h03vr3d2b6pv5rm65lsnkyx4caxxcdii4jzm")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -5365,12 +7892,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5")))) + (base32 "04cmgg5mw1cqbg95zyfc2imykmdxyff16w26rq97xghcxwiq2b3z")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs @@ -5392,12 +7919,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.4.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7")))) + (base32 "1n6v8a7c27aswmbrlcwcpghf27aplkc6nn923imglc3c0sh2lkrz")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -5443,14 +7970,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb")))) + "0yn348kmw7v46iym913ncx4yh5nxzmba8bdys52s12ldgjja53gp")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs @@ -5474,14 +8001,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr")))) + "1b8982fj0r7igj749wljsdfn3c985w8n3d5gbhr5rw73llfb8x6w")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -5511,14 +8038,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.14.4") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9")))) + "168g3xkhjzrfjpa1ynifdyfhsxx3rpyrbybsarlzr9kslw1cdkxl")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -5558,14 +8085,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq")))) + "0lp2gmjlsk1yqxim5pi26i27iijw11lrcxmji7ynlag359yfnynd")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -5607,14 +8134,14 @@ annotations and ontologies.") (define-public r-abaenrichment (package (name "r-abaenrichment") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 - "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c")))) + "15v5n6d3mnj9d86swkh9agfvrsd065dldaywm1adwmkhhk525wmd")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs @@ -5664,14 +8191,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224")))) + "18dd8saqx17fplvv5sbfz4p9fy7ksy3n9348rd3qlczihcrh9i3w")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -5689,14 +8216,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl")))) + "1mn6975npncmfjlpjs3s2pgsrm32xgvnyl2vh1922l6vra97dkrc")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -5732,14 +8259,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx")))) + "0qdac3qalcki20r90k40cc8d0lfywzn9pffg9d719yvs7nrsfdjr")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -5771,14 +8298,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.32.0") + (version "4.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww")))) + "1z3cxxg593d66nczz5hh2hdj1d87wc0lxrzc5sn6bp43n351q8h3")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -5810,14 +8337,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w")))) + "1al615x778h17jqiyhiyf6djaq9iygs1hlbrna6y4xc0f2kvgxld")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -5844,14 +8371,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw")))) + "0l5271cpzjlm4m0v6xcdg2vxlbhn53x1fd59ynb9jwll93av5h1f")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) @@ -5873,14 +8400,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801")))) + "0jr11c9hz7m49xc8pi6xrr5fhbv68vafvqpzhr0pmm51vvr1vfs9")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -5912,14 +8439,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb")))) + "1xfkgjlm0rxz82qcaqzx95cwirxifd9dsswjg3zcqmz03v7a0gz2")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -5961,14 +8488,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00")))) + "1z4abw9s2hs3csnx25nli7fpvb3rh3l0swzl0wfqp087fcs78pxi")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -6047,14 +8574,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2")))) + "1fkma2ic448h2lrlza8ipg65gpfsz4fhlxcnjpmzhhmzp2xi2p4a")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -6080,14 +8607,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp")))) + "1x07l255x52z6cgdc2j8285shqszhr034xm5686rp6d35vah55ji")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -6117,14 +8644,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw")))) + "0vp0n90rvjm8rzwkbrxa3fasb9val56bz2srz72xwsl3jzb5yk6w")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -6185,14 +8712,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3")))) + "1cs32sig1yvqn9xs0cvhfpmkh2lbllx7aab80sz58x03wnx8v60z")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -6209,14 +8736,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.12.0") + (version "3.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv")))) + "1g8k90p0sbcb3rdrbldj5bcjp2piy5ldni4jplyr78vjpmrmvqk7")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -6249,14 +8776,14 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wrench (package (name "r-wrench") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx")))) + "0yssmqayaryrc0asjjqxdipqdfg309llrzldx38jrfgdsza6bvs0")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs @@ -6275,14 +8802,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad")))) + "13f3g6fcc29k0g21mhnypm3nc6qqjw867vamvfkdzynspsfb32ga")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -6309,14 +8836,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w")))) + "186xgpgyfyi4angxhz6558lfpzvvszzlpyfr8xnbccs3gshk3db2")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -6330,14 +8857,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj")))) + "1mpdw477j78s2nvlf2lzm6mdjcpamyyazjn060h9q3apawn6zajx")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) @@ -6360,17 +8887,50 @@ deployed as a centralized bioinformatics resource for use by many users. Currently only Affymetrix oligonucleotide analysis is supported.") (license license:gpl2+))) +(define-public r-zinbwave + (package + (name "r-zinbwave") + (version "1.14.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "zinbwave" version)) + (sha256 + (base32 + "1y8krazz2qdn0wn8ijjs2gn5dl5l960v6bijbkvh0r8066l7viky")))) + (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))) + (native-inputs + `(("r-knitr" ,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 +negative binomial model that can be used to provide a low-dimensional +representations of single-cell RNA-seq data. The model accounts for zero +inflation (dropouts), over-dispersion, and the count nature of the data. +The model also accounts for the difference in library sizes and optionally +for batch effects and/or other covariates, avoiding the need for pre-normalize +the data.") + (license license:artistic2.0))) + (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm")))) + "1k7xaxr2gn26y8bps5l32g2axfhdn07nbk4q3qcx32d5jm75qkx2")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -6392,14 +8952,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5")))) + "0r5yqjal48xlcv5cidi7p3zwygvsllmv2zzkwkc9kfq083l2i4ih")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs @@ -6417,14 +8977,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7")))) + "10vpjvl4wps857xiy8rpzr82jzdfbc5rgwh3ir3my26lfws4hfz8")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -6447,14 +9007,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95")))) + "0ni3vblcadhwxaq1pf1n9jn66cp3bqch68ww4c8zh19zagil2y7r")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -6470,14 +9030,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "1.14.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1")))) + "0ymg4hmabk233qgassld62achjylm12rnidxbakfkx4dvvlbhxxv")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -6485,6 +9045,7 @@ Infinium HumanMethylation 450k assay.") ("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))) @@ -6502,14 +9063,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q")))) + "1haj25c4cmmjjvh181b41a9pvkh92f7k2w4ljn17iqg31vm45za1")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -6532,14 +9093,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507")))) + "0mfikbrs28q7r3lnsq0jma5x6nkrnm3q46242jh35w9c969jk5yy")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (inputs @@ -6557,14 +9118,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx")))) + "0i1yaw8h8gibakvaf1xd6nnjx2bsb2s9c0q74rbq9lm7haihivp6")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs @@ -6600,14 +9161,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb")))) + "1hqahh5h22mj2crqp6r9xnm111xmfgk39c100rcaziqrpdy5npk8")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments @@ -6640,14 +9201,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8")))) + "1635ff11ahzjrh3cdcxrq5bgd100n444k7mc0maz0jx21vj8qqb1")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs @@ -6659,13 +9220,11 @@ index.") ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicfiles" ,r-genomicfiles) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rbowtie" ,r-rbowtie) - ("r-rhisat2" ,r-rhisat2) ("r-rhtslib" ,r-rhtslib) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) @@ -6685,14 +9244,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9")))) + "02hwj2vd003x0zf273ndnwh7kxy6wc3sz14d3kryp2w2aqjj826f")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -6728,14 +9287,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.22.0") + (version "3.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw")))) + "0p6mr67mkw54490sv4dvkyh8l0xkpjfbqy532vi8l41i40qg3gry")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs @@ -6786,14 +9345,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4")))) + "1hyk40xgmy50rqxwdvc64d3pgz5vsg8vmlj5cp5m0n5m0adxcdfj")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs @@ -6823,14 +9382,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5")))) + "1j99kdywyljqzdcns5ysh590w4w8iiwzpddpfk5c8d4whax7vk5b")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -6861,14 +9420,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn")))) + "159fbkymn92li7dinsm56nsacjp8wnhsljv7airgs9m82p8wd5sl")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -6894,14 +9453,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.16.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9")))) + "1ls1qdfppcxysggi3bghrnspb5a3s40pm2mj4x0whc7c40cf90mg")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -6935,14 +9494,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.4.3") + (version "2.6.4") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0c4akc89p5467n5rzq9bi7h0h15rbpqpvh7fw42qcj7g2vc41wba")))) + "043m4512q73x6q529hqfgrap0fq5anvny4va085nafia06b805pi")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -6961,14 +9520,14 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09")))) + "1sdwgyvrsz0pp60zdfrcgb7bs8s87j7257p8ck813ydizc324x9w")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs @@ -6987,14 +9546,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp")))) + "163nr50nyvwrsajmm0cgxp70pqk61mgw0k7ams694hcb42162j8b")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -7012,30 +9571,18 @@ cluster count and membership by stability evidence in unsupervised analysis.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.2.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r")))) + "0wl7zqwv0i38dfzqfsz40n3mcbxi38ffn1rbd5pm9s7hq16zr4nv")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars.in" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a"))) - #t))))) (native-inputs - `(("r-knitr" ,r-knitr) - ("pkg-config" ,pkg-config))) + `(("r-knitr" ,r-knitr))) (propagated-inputs `(("r-bh" ,r-bh) ("r-rcpp" ,r-rcpp) @@ -7053,14 +9600,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8")))) + "13xpbkxi53rxmhvpdiy6bydmhicmxd2gi96d9c1qx4lkss2f14nc")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs @@ -7085,14 +9632,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734")))) + "1awskkq48qhv4v9glxgfqi0kgwqd62fbj641k4vvxfcwsf2c7bfg")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -7111,27 +9658,16 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac")))) + "1lm88qnfv6rnnr7wmgbvwyj272imjjjn7h3agxqqzsbmn8vyrnf0")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a"))) - #t))))) (propagated-inputs `(("r-bh" ,r-bh) ("r-biobase" ,r-biobase) @@ -7153,14 +9689,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m")))) + "0jd6m84m4znnpix4bcgdby7mnflsn206f5x2vw9n8rxnwzx77wpg")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -7190,14 +9726,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k")))) + "17x04xwyw2pp5zkhgvrmxkb8cbrv9wql6xhjsfpq0n6yd9dxqc1v")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs @@ -7221,14 +9757,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq")))) + "03xsmprrkxwkaksjlaxwp54mqfb3zlg6dbqhp87w78fwscisv76b")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -7261,14 +9797,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz")))) + "1hyds97ay4mn7nl830yh9v8mlasgsljsx5wsrhz2zsmbbyx6wbnb")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -7277,8 +9813,7 @@ model with Box-Cox transformation.") (add-after 'unpack 'unpack-bundled-sources (lambda _ (with-directory-excursion "src" - (invoke "tar" "xf" "protobuf-3.10.0.tar.gz")) - #t))))) + (invoke "tar" "xf" "protobuf-3.13.0.tar.gz"))))))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/RProtoBufLib/") @@ -7291,27 +9826,16 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.2.0") + (version "4.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag")))) + "1a9qb2dcvwgb3z0vdbbzn1rzy77d3da72kirs272344hdx9b2cx9")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\{h5lib\\}" match) - (string-append match "/libhdf5.a"))) - #t))))) (propagated-inputs `(("r-aws-s3" ,r-aws-s3) ("r-aws-signature" ,r-aws-signature) @@ -7320,6 +9844,7 @@ for other R packages to compile and link against.") ("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) @@ -7336,6 +9861,7 @@ for other R packages to compile and link against.") ("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 @@ -7354,14 +9880,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.2.0") + (version "4.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x")))) + "1yr5m7qmhmm52c70z3d0zy4zgf0hja7r2ig9yljv5w86bzm962x6")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs @@ -7390,14 +9916,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v")))) + "1par1d5pk1rjg15q7i5z5wqma7xg6fycb826a823wk8wr52a885x")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs @@ -7434,27 +9960,16 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.2.2") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "0ckjb7bkz0cy46scrv4vl9w37g54c0yihvzmbkzilip1ikpvhxd1")))) + "0ixy7mmnipk8wy61wz6qy7jfbc5zhs6p5iqaii8hdprjnb841ri7")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars.in" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\{h5lib\\}" match) - (string-append match "/libhdf5.a"))) - #t))))) (inputs `(("libxml2" ,libxml2) ("zlib" ,zlib))) @@ -7498,25 +10013,38 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "1.22.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf")))) + "18h7p7g3w9imyd1c93jllgp4kd74z96cs85wcqfhmd26nx18hl82")))) (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-tsne" ,r-tsne) + ("r-rlang" ,r-rlang) + ("r-rtsne" ,r-rtsne) + ("r-scattermore" ,r-scattermore) + ("r-tidyr" ,r-tidyr) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/FlowSOM/") (synopsis "Visualize and interpret cytometry data") @@ -7528,18 +10056,19 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.14.0") + (version "6.16.3") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q")))) + "1x6dbw4q6p9vngm256fr96r9fjxk5nik5ivkhbl5a9zqyq8wagpa")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs - `(("r-corpcor" ,r-corpcor) + `(("r-biocparallel" ,r-biocparallel) + ("r-corpcor" ,r-corpcor) ("r-dplyr" ,r-dplyr) ("r-ellipse" ,r-ellipse) ("r-ggrepel" ,r-ggrepel) @@ -7573,14 +10102,14 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469")))) + "04vxc43p3kpsx0vksk2nwmy9p56h35z2mc8j9p2wm29zaz1y8j3p")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs @@ -7619,24 +10148,29 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf")))) + "1yh0l11vnslgr6zsbpgc8mc4aa32zy34f5yrz98hkcdl53iw5y7f")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs - `(("r-aucell" ,r-aucell) + `(("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-summarizedexperiment" ,r-summarizedexperiment) + ("r-tibble" ,r-tibble))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://aertslab.org/#scenic") @@ -7653,17 +10187,43 @@ each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).") (license license:gpl3))) +(define-public r-chicago + (package + (name "r-chicago") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Chicago" version)) + (sha256 + (base32 + "0dkwy6pfvzd7g4qmhjl24ypn92l78w1zy0ajhcxgg39f7zsq883x")))) + (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))) + (home-page "https://bioconductor.org/packages/Chicago") + (synopsis "Capture Hi-C analysis of genomic organization") + (description + "This package provides a pipeline for analysing Capture Hi-C data.") + (license license:artistic2.0))) + (define-public r-cicero (package (name "r-cicero") - (version "1.8.1") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr")))) + "1y34cm52bv1v2hr7sz8zjzxwd4wng7v75avz5wx45l0ld54z9l10")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -7723,14 +10283,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8")))) + "1hif40vfg2lkbyf6abbkxbdm3b1biw6gxnh6ca2sydvi3y5l2ys2")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) @@ -7767,18 +10327,63 @@ accessibility data.") (description "@code{r-circrnaprofiler} is a computational framework for a comprehensive in silico analysis of @dfn{circular RNA} (circRNAs). This computational -framework allows to combine and analyze circRNAs previously detected by +framework allows combining and analyzing circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.") (license license:gpl3))) (define-public r-cistopic - (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") - (revision "0")) + (package + (name "r-cistopic") + (version "2.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aertslab/cisTopic") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "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))) + (home-page "https://github.com/aertslab/cisTopic") + (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") + (description + "The sparse nature of single cell epigenomics data can be overruled using +probabilistic modelling methods such as @dfn{Latent Dirichlet +Allocation} (LDA). This package allows the probabilistic modelling of +cis-regulatory topics (cisTopics) from single cell epigenomics data, and +includes functionalities to identify cell states based on the contribution of +cisTopics and explore the nature and regulatory proteins driving them.") + (license license:gpl3))) + +(define-public r-cistopic-next + (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803") + (revision "1")) (package - (name "r-cistopic") - (version (git-version "0.2.1" revision commit)) + (inherit r-cistopic) + (name "r-cistopic-next") + ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd + ;; since the previous release is 2.1.0. Oh well. + (version (git-version "0.3.0" revision commit)) (source (origin (method git-fetch) @@ -7788,13 +10393,13 @@ analysis, evolutionary conservation, biogenesis to functional analysis.") (file-name (git-file-name name version)) (sha256 (base32 - "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8")))) - (build-system r-build-system) + "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2")))) + (properties `((upstream-name . "cisTopic"))) (propagated-inputs `(("r-aucell" ,r-aucell) ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) ("r-dosnow" ,r-dosnow) + ("r-dplyr" ,r-dplyr) ("r-dt" ,r-dt) ("r-feather" ,r-feather) ("r-fitdistrplus" ,r-fitdistrplus) @@ -7805,32 +10410,27 @@ analysis, evolutionary conservation, biogenesis to functional analysis.") ("r-plyr" ,r-plyr) ("r-rcistarget" ,r-rcistarget) ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://github.com/aertslab/cisTopic") - (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") - (description - "The sparse nature of single cell epigenomics data can be overruled using -probabilistic modelling methods such as @dfn{Latent Dirichlet -Allocation} (LDA). This package allows the probabilistic modelling of -cis-regulatory topics (cisTopics) from single cell epigenomics data, and -includes functionalities to identify cell states based on the contribution of -cisTopics and explore the nature and regulatory proteins driving them.") - (license license:gpl3)))) + ("r-s4vectors" ,r-s4vectors) + ("r-text2vec" ,r-text2vec))) + (native-inputs + `(("r-knitr" ,r-knitr)))))) (define-public r-genie3 (package (name "r-genie3") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5")))) + "1v54dzcz654wfm3npbp8gb55v49im0fm547cz3hvsidq4zhi3l1b")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) - (propagated-inputs `(("r-reshape2" ,r-reshape2))) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GENIE3") @@ -7843,14 +10443,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.66.0") + (version "1.68.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9")))) + "1rmsrvn6hrg9ay7xfb05mfkxknnig78p3kbk9ghsd11lhx2fjm3s")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (propagated-inputs @@ -7891,14 +10491,14 @@ data.") (define-public r-watermelon (package (name "r-watermelon") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f")))) + "1qar8z0nf33bqr488swig0bfq8lnvcdjcxvw3q3b0hkkvybn27zw")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -7928,14 +10528,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.26.1") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n")) + "1w3z718q3bhh8bp71va9pbcd62pwbvgjw33ffg960jya40xssvc7")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -7948,7 +10548,7 @@ metrics, with methods for objects produced by the @code{methylumi} and (substitute* "src/Makevars" (("all: \\$\\(SHLIB\\)") "all:") (("\\$\\(SHLIB\\): liblzma.a") "") - (("(ZLIB|LZ4)/.*") "") + (("^ (ZLIB|LZ4)/.*") "") (("CoreArray/dVLIntGDS.cpp.*") "CoreArray/dVLIntGDS.cpp") (("CoreArray/dVLIntGDS.o.*") @@ -7957,8 +10557,7 @@ metrics, with methods for objects produced by the @code{methylumi} and "PKG_LIBS = -llz4")) (substitute* "src/CoreArray/dStream.h" (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) - (string-append "include <" header ">"))) - #t)))) + (string-append "include <" header ">"))))))) (properties `((upstream-name . "gdsfmt"))) (build-system r-build-system) (inputs @@ -7987,14 +10586,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7")))) + "061f0hc4m4nvdr6298pg3inpx1z2bpsm9nlxqs3v7n58q15xyzri")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -8015,14 +10614,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2")))) + "06w43plv4x1pafybq633n7adqp9yj3bvaaamq7vylmkfbcx3nl8k")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs @@ -8079,14 +10678,14 @@ injected in that sequence).") (define-public r-reqon (package (name "r-reqon") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq")))) + "1z13avbxwvvhh03arjfnaipznynifsi8k2hzw4kappz24f7lwmza")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs @@ -8104,14 +10703,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi")))) + "1sydzrqydfv1ik2h08xkxlx6xrv866bf0if6v5wch9l3krh0sych")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -8151,14 +10750,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.8.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn")))) + "1095a2ynxcf9xiac5cjzslcbmjnjpbby0vy7d84qagdiq1w6mrhn")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) @@ -8192,14 +10791,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5")))) + "0abhrk53csd9jz9sv4q1qr74jax9mbj2icbz1iilf1123nvnjypd")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -8298,14 +10897,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah")))) + "1pqy2g9pg8pswmkrs2fzlkwwliw2r7f33h05bci5bz41b8ribpzj")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -8342,14 +10941,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji")))) + "1y3ik5a9w66jby6682jfm8mn2883s8yfv4xw8a8v1f6q2d1j938l")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs @@ -8376,14 +10975,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv")))) + "1clcz610sl3s0mjf84j21xgrmjhkxcc4h292ljwq5yzbkk68g896")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) @@ -8401,14 +11000,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.8.4") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "0pmi5mp5v0srr482vlkfmkp28bywq969fvv9g5kjl5rxki963zmr")))) + "0hv2v2zgif5ihr5hxmdz32rln43jc1j0rslp44kd3rijjl45zysn")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -8423,12 +11022,10 @@ data.") `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-ggplot2" ,r-ggplot2) - ("r-ggseqlogo" ,r-ggseqlogo) ("r-iranges" ,r-iranges) ("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp) ("r-rcppthread" ,r-rcppthread) - ("r-rdpack" ,r-rdpack) ("r-rlang" ,r-rlang) ("r-s4vectors" ,r-s4vectors) ("r-yaml" ,r-yaml))) @@ -8517,14 +11114,14 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50")))) + "1gp40ddspblpszzm4k4r7ysgx883iwdfqc5ds23p2q1ml9idwgvv")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs @@ -8539,14 +11136,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im")))) + "18n6j2ihv85rhai5sf5k3mwf9nkc2nl2sinx3rrs6sbl529g4mw4")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs @@ -8564,14 +11161,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn")))) + "0aaawm7h3ppyyhd7hi14rpynagnxx4730f5vxizj5bpzwbclp6h9")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") @@ -8590,14 +11187,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k")))) + "0j3gs4xcdgaca2c62jf2h86skbbxm1c9g2khs5bsa8fmkskr6vl9")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs @@ -8614,14 +11211,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a")))) + "1fwy7ws0bn67557s0kcw8pbln2jg834n6kfbs8297ps07nxr0lpj")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs @@ -8644,19 +11241,18 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61")))) + "017xwra6ms7kx6sg3ksw1vr9zn23imc2qjgpmjikx7mgbak125xh")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs - `(("libsbml" ,libsbml) - ("zlib" ,zlib))) + `(("libsbml" ,libsbml))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-graph" ,r-graph))) @@ -8672,14 +11268,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97")))) + "01knpd964m2g9vwd7c72qnc8g2p2pzhvk7lin4mhvcmb3pvsdlh7")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs @@ -8694,14 +11290,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz")))) + "1qkxixkgvvfha0ii8rwwcbrbjmbbxsy8afv5ymcq01k3hbykx44r")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs `(("graphviz" ,graphviz))) @@ -8718,14 +11314,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y")))) + "1y9659pxm65w51zvrz36girb3qvfc64zijjkxmg6xn4pbc8vv1wf")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs @@ -8782,14 +11378,14 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis")))) + "0yrg9x1a92zmz7j5hk77cph1jg82mkpr7k7qi9fdr6z5nqq6fgz6")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs @@ -8825,14 +11421,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.42.2") + (version "3.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9")))) + "1z59npqk7hnqzhjdnry6lfqlyxfzwqprp7bmbdzs4rp22pzcv1v8")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -8866,14 +11462,14 @@ structures.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.28.2") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5")))) + "1mlv80w8a7l8cii3dfqvanvh0qdqvcg8c1iiq4xlyvkjxfs64ka1")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -8901,14 +11497,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv")))) + "1ybyhmrcvj6k1laxw9bc8jbn533frkzh9k8kl1ibd5pi368rfqzn")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs @@ -8933,14 +11529,14 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk")))) + "11bgz6951nfygxp3fm0190gf2bb5zplis1bc0am4757liw4qybhf")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs @@ -8949,6 +11545,8 @@ visualize bioinformatics analyses.") ("r-graph" ,r-graph) ("r-httr" ,r-httr) ("r-rappdirs" ,r-rappdirs))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description @@ -8960,14 +11558,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m")))) + "1293z89ai766c559axgr7mz5x4564gyl9xqzf6s8s0aj1xb35gqf")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -8992,14 +11590,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd")))) + "1k1kl0m7wzaqpv7i20pfav2a6jf93bhri4w7qdikmvkf011n9422")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs @@ -9038,35 +11636,16 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib")))) + "1h0l5w33c9jpc20pynq634qmx8jbfa802d7jslmf4haljmrxm4a1")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - ;; This package can be used by calling BiocCheck(<package>) from - ;; within R, or by running R CMD BiocCheck <package>. This phase - ;; makes sure the latter works. For this to work, the BiocCheck - ;; script must be somewhere on the PATH (not the R bin directory). - (add-after 'install 'install-bioccheck-subcommand - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (dest-dir (string-append out "/bin")) - (script-dir - (string-append out "/site-library/BiocCheck/script/"))) - (mkdir-p dest-dir) - (symlink (string-append script-dir "/checkBadDeps.R") - (string-append dest-dir "/checkBadDeps.R")) - (symlink (string-append script-dir "/BiocCheck") - (string-append dest-dir "/BiocCheck"))) - #t))))) (propagated-inputs `(("r-codetools" ,r-codetools) ("r-graph" ,r-graph) @@ -9087,14 +11666,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75")))) + "12bmj9kdlylp02cfwviak7y323ndccl2694rvi4cdg4vsx7v3ya3")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs @@ -9112,13 +11691,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.18.1") + (version "2.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp")))) + "0p2wdq5vrx63ndghl9ww428z2lwnv5y88xmcr51by2g6vcj3brcf")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -9140,13 +11719,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.58.1") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4")))) + "0pc5ll59vm8a9s1nrdc7p9wk11a52rrz669fsrrqd8qapa8p6wfd")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -9168,14 +11747,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "1.16.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg")))) + "1mzmw3100lf33yhz27nbxncrjk5bprlackrjcwf8xdhcaidg40p4")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -9202,14 +11781,14 @@ access.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx")))) + "1h63vg1iskw79ijg5h1b9097ams8pp3kvnlawlfci6xfli07xpkj")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -9229,14 +11808,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs")))) + "0l0arf3q1f6zy6pdgsy3h5n523sg1hlilv7lj7snr5814idgdj51")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) @@ -9264,14 +11843,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108")))) + "1ix09a39z7y2cj0y8qsd66ka8a8y8q79w08l4jv1yhhn9h4va89s")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs @@ -9309,14 +11888,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19")))) + "135rga7mwpzy8ypvriqpbmlh9l5yf61s9s1sa9615qfab14jh06b")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs @@ -9338,14 +11917,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.8.0") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m")))) + "1sfp1nxlwbbbpx2iwvyk9p10jdy2vxhgn2b5fy5blayzjjlb3d80")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs @@ -9362,10 +11941,8 @@ gene selection, testing relationships, and so on.") ("r-igraph" ,r-igraph) ("r-jsonlite" ,r-jsonlite) ("r-magrittr" ,r-magrittr) - ("r-rappdirs" ,r-rappdirs) ("r-rbgl" ,r-rbgl) ("r-readr" ,r-readr) - ("r-rex" ,r-rex) ("r-rlang" ,r-rlang) ("r-rvest" ,r-rvest) ("r-stringr" ,r-stringr) @@ -9388,14 +11965,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.4.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg")))) + "0nmrg9cgq8l9w467y364jghnvym05abpj8pyj90grmrib2xc5sj2")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -9426,14 +12003,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6")))) + "1a32bwgnxaw0gv2gij2p4rm0a6l06jjhidvfz2v4k900pz1w79av")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) @@ -9459,14 +12036,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap")))) + "1y1x9q9aa76gbhsyfn638rxp5icjvq30fv3a4205xh7g5jwlf6yw")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs @@ -9482,14 +12059,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb")))) + "11idi9fwvyhkakbm63qxcdhkany8gbskis04z0p5a39lppq8ks31")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs @@ -9528,14 +12105,14 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj")))) + "0ads9c9i8b39wvjih057zlyivj8zpsqjxf6r97yflz4sbi1jmcji")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs @@ -9556,14 +12133,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5")))) + "17gj4haa4ywc6bmppm342jzppl3inqa94235yspikij6c098vrmc")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs @@ -9589,14 +12166,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr")))) + "1rzgwxx4w2bqsaz0xmkhi4w9zsxgms80xf59zg1xp1camyhaihlz")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs @@ -9719,14 +12296,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.52.1") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll")))) + "17a00blz4kvhmsk92bp5alj9kdpy7h1id7nk4vqxakhkb2jabr20")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -9740,13 +12317,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.28.1") + (version "0.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) + "103sw0fmmm4f3hprrsn7dwg0kmmr9mcmb46dcwwb6p5np0al2sfx")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -9807,14 +12384,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77")))) + "0d0xq1vgr4b165cn4wg7zmfjyc1d9ir4amgs196j4cgrhpmrnl8s")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments @@ -9845,13 +12422,13 @@ objects from the @code{graph} package.") (define-public r-fithic (package (name "r-fithic") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2")))) + "1p8a6lis5yswaj647bjw89harlarnsxmvjzz63fn1l6gxrwhh8bx")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -9871,13 +12448,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy")))) + "0s3kfqs3zlmq61hxdmxpmi9gfs9w3byckw7xzp1hrhdbsl46yvgq")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -9900,27 +12477,16 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g")))) + "1718hplz5qlbwxwb87509bl7lir9kilvn1s7p2haz551pg48zvrc")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5LIB_LIBS\\)" match) - (string-append match "/libhdf5.a"))) - #t))))) (inputs `(("zlib" ,zlib))) (propagated-inputs @@ -9929,6 +12495,7 @@ provided.") ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-rhdf5" ,r-rhdf5) + ("r-rhdf5filters" ,r-rhdf5filters) ("r-rhdf5lib" ,r-rhdf5lib) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/HDF5Array") @@ -9941,22 +12508,21 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.12.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28")) + "1cwynbcaaxmbh45fc0d264liqdj0wbjlj7k2bsq3qfjbnh6kkam5")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled binaries (delete-file-recursively "src/wininclude/") - (delete-file-recursively "src/winlib-4.9.3/") (delete-file-recursively "src/winlib-8.3.0/") - (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") + (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz") #t)))) (properties `((upstream-name . "Rhdf5lib"))) (build-system r-build-system) @@ -9968,7 +12534,9 @@ block processing.") (for-each delete-file '("configure" "configure.ac")) ;; Do not make other packages link with the proprietary libsz. (substitute* "R/zzz.R" - ((" \"%s/libsz.a\"") "")) + ((" \"%s/libsz.a\"") "") + (("patharch, .getDynamicLinks") + ".getDynamicLinks")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) @@ -10007,12 +12575,10 @@ block processing.") (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) ;; szip is non-free software (("cp \"\\$\\{SZIP_LIB\\}.*") "") - (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) - #t))))) - (inputs - `(("zlib" ,zlib))) + (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))))))) (propagated-inputs - `(("hdf5" ,hdf5-1.10))) + `(("hdf5" ,hdf5-1.10) + ("zlib" ,zlib))) (native-inputs `(("hdf5-source" ,(package-source hdf5-1.10)) ("r-knitr" ,r-knitr))) @@ -10025,19 +12591,20 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.6.4") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji")))) + "06bpfpddsl49csxrs8hlx5pv0absc2wdcparchf8qqaqydazwci2")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix))) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/beachmat") @@ -10053,13 +12620,13 @@ matrices.") (define-public r-cner (package (name "r-cner") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c")))) + (base32 "13w0gsfm7k29dp5nb0c9sb2ix506ph6dixsjis6xxcz6acq7lg2k")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -10101,14 +12668,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha")))) + "1avgjv2nyr28cla0z9dvh3v0hr1f561sz2as1k53a42irbjk0var")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs @@ -10147,14 +12714,14 @@ provides a wrapper of de novo motif discovery software.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z")))) + "1vif3dp4lv4jz1pxsq0ig791ir8q65jmrlqmkyfxpfxfj5alqnbm")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs @@ -10181,13 +12748,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819")))) + (base32 "1birmwvcvl2hb5ygbsb3wvbdfayqqs53j1bks46cbkq7ybigfyar")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -10228,19 +12795,21 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.12.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2")))) + "1bwdhx0ss0s8f4xdgwd7x48apn849x4dyb5hbyglcz31r5vh1qgz")))) (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))) (native-inputs @@ -10257,14 +12826,14 @@ libraries.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.0.4") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8")))) + "015k879gg2r39lp6mz26jwmysa56k0ial6v74zzmbi8hnz9zic3i")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -10292,16 +12861,17 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.18.6") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0k1ls5gqv1zsn1w2kszhmbhwfccfjw8khk36s5zbf90rbbkw5609")))) + "1046fgf93dda3y2z5ilrjdczz7klj67ag63p4p1h03965wpj9vfn")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) + `(("r-beachmat" ,r-beachmat) + ("r-biocgenerics" ,r-biocgenerics) ("r-biocneighbors" ,r-biocneighbors) ("r-biocparallel" ,r-biocparallel) ("r-biocsingular" ,r-biocsingular) @@ -10311,7 +12881,9 @@ of other packages.") ("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) @@ -10329,20 +12901,19 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.18.5") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1")))) + "0ilzp6ngw9pq88gk79iic2zxfh5jaic6lnq3xfwc9a269bjylff0")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) ("r-bh" ,r-bh) ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) ("r-biocparallel" ,r-biocparallel) ("r-biocsingular" ,r-biocsingular) ("r-bluster" ,r-bluster) @@ -10353,6 +12924,7 @@ quality control.") ("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) @@ -10372,14 +12944,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.2.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii")))) + "0b22kzg751zlkcbs8pi0bcqrsj3imsg35qfvxfrqb7gav7qznc8v")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) @@ -10400,21 +12972,19 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.12.3") + (version "1.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h")))) + "1zxs2wjnsq9w1cl4andsd7y9xsdnl1an55khw9viaq758m7hhbcn")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-delayedarray" ,r-delayedarray) - ("r-hdf5array" ,r-hdf5array) + `(("r-delayedarray" ,r-delayedarray) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-matrixgenerics" ,r-matrixgenerics) @@ -10438,18 +13008,19 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630")))) + "13g8a726vsyjs6m1kd42vf8avdnmhykxhl6z3j2njzkp2jg17pd8")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) + `(("r-clue" ,r-clue) + ("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors))) (native-inputs @@ -10469,21 +13040,19 @@ within the R for Mass Spectrometry packages.") (define-public r-biocio (package (name "r-biocio") - (version "1.0.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18")))) + "0skwnpxl6fkqihidpqrfzzh7b05x11j6jwkiinmhggmv0ggjb5ph")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-rcurl" ,r-rcurl) - ("r-s4vectors" ,r-s4vectors))) + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocIO") @@ -10505,14 +13074,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx")))) + "0555a3riyp781mlffmnf93igfq8vl8wjk51pa9qb48qkdn6y8pfc")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs @@ -10531,14 +13100,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j")))) + "11vhy1l6za73dpdj85q4ksaghgd8vb2h8v9iirmsn2vpajqrvgjh")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs @@ -10550,7 +13119,7 @@ experiments, and visualize de influence of the involved factors.") "https://bioconductor.org/packages/msmsTests") (synopsis "Differential LC-MS/MS expression tests") (description - "This packages provides statistical tests for label-free LC-MS/MS data + "This package provides statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR @@ -10563,14 +13132,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.14.0") + (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh")))) + "1vw8x54hwgcyn29k81zcvawawy2iy2qgp49gjpb830q04gx6yc6h")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -10621,14 +13190,14 @@ standards, ii) single-cell deconvolution, and iii) bead-based compensation.") (define-public r-erma (package (name "r-erma") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k")))) + "02a9702sasgighwb0f9ii8n30ngfx1hjnppaay1f5zsigr8vqalz")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10661,14 +13230,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) + "0k3dxacrwgyrkvm7ggc2s1s1pbfs6c0a7ngykkj7jnc73czvnilx")))) (build-system r-build-system) (arguments `(#:phases @@ -10829,14 +13398,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.34.1") + (version "1.36.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0bmlfz9ri1gkwyl605a2hqi5b8jdpvynrxwghwmrsd657ip6c7n1")))) + "0lp0k8jd4dfsfn10706124graaqnzcyv1siblvm8dn2ykw2rc6vl")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -10878,17 +13447,18 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna")))) + "0109cxsviq1sk5hfwkjzd0y1kpm934287asjjd0j8jhh4b0ah2b2")))) (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) @@ -10911,18 +13481,19 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v")))) + (base32 "0zxdph5hzr3kzj2g1mjqpiviwa189a5sq4bw7wiry6r79fdnklqs")))) (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))) (home-page "https://bioconductor.org/packages/KEGGgraph") (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor") @@ -10937,14 +13508,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.20.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm")))) + "16vp5psmigxdkkd6fbivb6s8mvd7rsnm771wsbjvayl2y7ig7kq4")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -10996,16 +13567,80 @@ optionally include the physical locations or genetic map distances of each SNP on the plot.") (license license:gpl3))) +;; This is a CRAN package, but it depends on r-rgraphviz, which is a +;; Bioconductor package. +(define-public r-abn + (package + (name "r-abn") + (version "2.5-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abn" version)) + (sha256 + (base32 + "1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw")))) + (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))) + (home-page "https://r-bayesian-networks.org/") + (synopsis "Modelling multivariate data with additive bayesian networks") + (description + "Bayesian network analysis is a form of probabilistic graphical models +which derives from empirical data a directed acyclic graph, DAG, describing +the dependency structure between random variables. An additive Bayesian +network model consists of a form of a DAG where each node comprises a +@dfn{generalized linear model} (GLM). Additive Bayesian network models are +equivalent to Bayesian multivariate regression using graphical modelling, they +generalises the usual multivariable regression, GLM, to multiple dependent +variables. This package provides routines to help determine optimal Bayesian +network models for a given data set, where these models are used to identify +statistical dependencies in messy, complex data.") + (license license:gpl2+))) + +;; This is a CRAN package, but it depends on r-rsamtools, which is a +;; Bioconductor package. +(define-public r-spp + (package + (name "r-spp") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (cran-uri "spp" version)) + (sha256 + (base32 + "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w")))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-catools" ,r-catools) + ("r-rcpp" ,r-rcpp) + ("r-rsamtools" ,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 +other functional sequencing data.") + (license license:gpl2))) + (define-public r-pathview (package (name "r-pathview") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4")))) + (base32 "1fank0qavv9ikmzxvms8mky2wbzny02rfqkvsqzma26r3vl4r1g1")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs @@ -11033,14 +13668,14 @@ large-scale and fully automated analysis.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24")))) + "11vvih5y9kvyjfp2navkfpp4xiyfgwlv4r0x3p52hkj92pc2pg3g")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -11060,14 +13695,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "0vgpb7g2cncdn82hia2yzzachyns2zbd7906662g990qjnp2xlm1")))) + "09cqzylci4x4i7wn4ckcqhdlljbzfrp08wdvkkc5vrdldnj9pq5h")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs @@ -11095,16 +13730,48 @@ export to genome browser viewable files, and functions for enrichment analyses.") (license license:artistic2.0))) +(define-public r-guitar + (package + (name "r-guitar") + (version "2.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Guitar" version)) + (sha256 + (base32 + "1q4m6c5181dw12lvdp324jlk78c9jgcsg6b9hk87zjadp6j0gfr6")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/Guitar") + (synopsis "Visualize genomic features") + (description + "This package is designed for visualization of RNA-related genomic +features with respect to the landmarks of RNA transcripts, i.e., transcription +starting site, start codon, stop codon and transcription ending site.") + (license license:gpl2))) + (define-public r-sushi (package (name "r-sushi") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p")))) + "1m5l0nflhcynb3gz7b8qzvknb0s6xhds8z1yl3mbv8ic9qn2knv4")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs @@ -11116,3 +13783,1002 @@ analyses.") "This package provides flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures.") (license license:gpl2+))) + +(define-public r-ballgown + (package + (name "r-ballgown") + (version "2.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ballgown" version)) + (sha256 + (base32 + "0ff8z4pfgzai2q4aafclg36bhsi9jwl9xhh1p9fqhmikisscq7i1")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/ballgown") + (synopsis "Flexible, isoform-level differential expression analysis") + (description + "This package provides tools for statistical analysis of assembled +transcriptomes, including flexible differential expression analysis, +visualization of transcript structures, and matching of assembled transcripts +to annotation.") + (license license:artistic2.0))) + +(define-public r-megadepth + (package + (name "r-megadepth") + (version "1.2.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "megadepth" version)) + (sha256 + (base32 + "0grgj7bzyqnxby0sx5ic1h9bzmx19xwl0a5b3v6wbnwqcla2i3kg")))) + (properties `((upstream-name . "megadepth"))) + (build-system r-build-system) + (inputs `(("megadepth" ,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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/LieberInstitute/megadepth") + (synopsis "BigWig and BAM related utilities") + (description + "This package provides an R interface to Megadepth. It is particularly +useful for computing the coverage of a set of genomic regions across bigWig or +BAM files. With this package, you can build base-pair coverage matrices for +regions or annotations of your choice from BigWig files.") + (license license:artistic2.0))) + +(define-public r-beclear + (package + (name "r-beclear") + (version "2.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BEclear" version)) + (sha256 + (base32 + "0w18livng2gcmjgvws7pix3gsnj237rs34sgwxsfmn8p5vfx8b30")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/uds-helms/BEclear") + (synopsis "Correction of batch effects in DNA methylation data") + (description + "This package provides functions to detect and correct for batch effects +in DNA methylation data. The core function is based on latent factor models +and can also be used to predict missing values in any other matrix containing +real numbers.") + (license license:gpl3))) + +(define-public r-bgeecall + (package + (name "r-bgeecall") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BgeeCall" version)) + (sha256 + (base32 + "1byciy7vzbdkdgaim10s9qb7zlxsywbhcsrka31gm0rm9ljqc665")))) + (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))) + (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 +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.") + (license license:gpl3))) + +(define-public r-bgeedb + (package + (name "r-bgeedb") + (version "2.18.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BgeeDB" version)) + (sha256 + (base32 + "1ziq180yfpdqwhjdzkwjjhwzn3kb0gkj6q0a26c7a30mcfb50w11")))) + (properties `((upstream-name . 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Its architecture as a development framework facilitates +the development of new database connectors for local projects or inside +separate published packages.") + (license license:agpl3+))) + +(define-public r-biomformat + (package + (name "r-biomformat") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biomformat" version)) + (sha256 + (base32 + "1wgshkddxbmpsihpkm0dp7vqp59ns6iqbx574y80n2pxb8dx8sy9")))) + (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))) + (home-page "https://github.com/joey711/biomformat/") + (synopsis "Interface package for the BIOM file format") + (description + "This is an R package for interfacing with the BIOM format. This package +includes basic tools for reading biom-format files, accessing and subsetting +data tables from a biom object (which is more complex than a single table), as +well as limited support for writing a biom-object back to a biom-format file. +The design of this API is intended to match the Python API and other tools +included with the biom-format project, but with a decidedly \"R flavor\" that +should be familiar to R users. This includes S4 classes and methods, as well +as extensions of common core functions/methods.") + (license license:gpl2))) + +(define-public r-mvcclass + (package + (name "r-mvcclass") + (version "1.66.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MVCClass" version)) + (sha256 + (base32 + "1di7y10mr7caacd6igwxnr62cm4v1x877yi4a2i5jqz1058jqni7")))) + (properties `((upstream-name . 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Finally, users can also +identify consensus modules across independent expression sets and calculate +intra and interspecies module preservation statistics between different +networks.") + (license license:gpl3))) + +(define-public r-bionet + (package + (name "r-bionet") + (version "1.52.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioNet" version)) + (sha256 + (base32 + "15rk1jfv4h1mxvr5bs0qmq6fdnza7zcmksigqxb46fs7f6znr3yi")))) + (properties `((upstream-name . 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By fitting a beta-uniform mixture model and +calculating scores from the p-values, overall scores of network regions can be +calculated and an integer linear programming algorithm identifies the maximum +scoring subnetwork.") + (license license:gpl2+))) + +(define-public r-bionetstat + (package + (name "r-bionetstat") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioNetStat" version)) + (sha256 + (base32 + "16xlfng9m8xvm831c2x6zmjc0gavlfiy9pnza55hdv86888fcnbg")))) + (properties `((upstream-name . 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"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))) + (home-page "https://code.nimahejazi.org/biotmle/") + (synopsis "Targeted learning with moderated statistics for biomarker discovery") + (description + "This package provides tools for differential expression biomarker +discovery based on microarray and next-generation sequencing data that +leverage efficient semiparametric estimators of the average treatment effect +for variable importance analysis. Estimation and inference of the (marginal) +average treatment effects of potential biomarkers are computed by targeted +minimum loss-based estimation, with joint, stable inference constructed across +all biomarkers using a generalization of moderated statistics for use with the +estimated efficient influence function. The procedure accommodates the use of +ensemble machine learning for the estimation of nuisance functions.") + (license license:expat))) + +(define-public r-bsseq + (package + (name "r-bsseq") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bsseq" version)) + (sha256 + (base32 + "1xpv85hr681kkkilsnasndkszwmzbzq11y0lff4na2ilsm7sqmmi")))) + (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))) + (home-page "https://github.com/hansenlab/bsseq") + (synopsis "Analyze, manage and store bisulfite sequencing data") + (description + "This package provides a collection of tools for analyzing and +visualizing bisulfite sequencing data.") + (license license:artistic2.0))) + +(define-public r-dmrseq + (package + (name "r-dmrseq") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "dmrseq" version)) + (sha256 + (base32 + "1jbbjifjsnk9261wqmdwkbzj1w52g6vaanpk4w816ri0fap587m4")))) + (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))) + (home-page "https://bioconductor.org/packages/dmrseq") + (synopsis "Detection and inference of differentially methylated regions") + (description + "This package implements an approach for scanning the genome to detect +and perform accurate inference on differentially methylated regions from Whole +Genome Bisulfite Sequencing data. The method is based on comparing detected +regions to a pooled null distribution, that can be implemented even when as +few as two samples per population are available. Region-level statistics are +obtained by fitting a @dfn{generalized least squares} (GLS) regression model +with a nested autoregressive correlated error structure for the effect of +interest on transformed methylation proportions.") + (license license:expat))) + +(define-public r-omnipathr + (package + (name "r-omnipathr") + (version "3.0.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "OmnipathR" version)) + (sha256 + (base32 "0rbq3h3cp5dgpy5ifmbnfm6z8w4jv45wjzyl1f4qacgrbyf2l30a")))) + (properties `((upstream-name . "OmnipathR"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (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))) + (home-page "https://saezlab.github.io/OmnipathR/") + (synopsis "OmniPath web service client and more") + (description + "This package provides a client for the OmniPath web service and many +other resources. It also includes functions to transform and pretty print +some of the downloaded data, functions to access a number of other resources. +Furthermore, OmnipathR features a close integration with the NicheNet method +for ligand activity prediction from transcriptomics data.") + (license license:expat))) + +(define-public r-biscuiteer + (package + (name "r-biscuiteer") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biscuiteer" version)) + (sha256 + (base32 + "0f4kk4v2c5diq0fbvyvgwjd1kjk9izr6n9wfrlrr7wbx4pz3c3h6")))) + (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))) + (home-page "https://github.com/trichelab/biscuiteer") + (synopsis "Convenience functions for the Biscuit package") + (description + "This package provides a test harness for bsseq loading of Biscuit +output, summarization of WGBS data over defined regions and in mappable +samples, with or without imputation, dropping of mostly-NA rows, age +estimates, etc.") + (license license:gpl3))) + +(define-public r-tximeta + (package + (name "r-tximeta") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "tximeta" version)) + (sha256 + (base32 + "0ipgpcl93cac4qff6lp9x2l3gav5kb1x1d56g32h09hlm797rvvh")))) + (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))) + (home-page "https://github.com/mikelove/tximeta") + (synopsis "Transcript quantification import with automatic metadata") + (description + "This package implements transcript quantification import from Salmon and +alevin with automatic attachment of transcript ranges and release information, +and other associated metadata. De novo transcriptomes can be linked to the +appropriate sources with linkedTxomes and shared for computational +reproducibility.") + (license license:gpl2))) |