diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 235 |
1 files changed, 186 insertions, 49 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 71037a86e2..534204a16a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,11 +1,11 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr> -;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> @@ -626,13 +626,13 @@ based on mapping using Entrez Gene identifiers.") (define-public r-org-hs-eg-db (package (name "r-org-hs-eg-db") - (version "3.7.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) (sha256 (base32 - "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) + "0mnddv42ll0sc0zxf7hkgilslykbvfn7xgxg1g8qi57q2dmpwb6j")))) (properties `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) @@ -956,6 +956,26 @@ annotations.") Disease Ontology.") (license license:artistic2.0))) +(define-public r-hgu133plus2-db + (package + (name "r-hgu133plus2-db") + (version "3.13.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hgu133plus2.db" version 'annotation)) + (sha256 + (base32 "0i6cfk7ahql4fcgrq0dai9gkjbsahyzd9iv4lqv1ad58fzkmipnx")))) + (properties `((upstream-name . "hgu133plus2.db"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi r-org-hs-eg-db)) + (home-page "https://bioconductor.org/packages/hgu133plus2.db") + (synopsis "Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data") + (description + "This package provides Affymetrix HG-U133_Plus_2 array annotation +data (chip hgu133plus2) assembled using data from public repositories.") + (license license:artistic2.0))) + (define-public r-pfam-db (package (name "r-pfam-db") @@ -1302,9 +1322,7 @@ downloaded from Encode.") (version "1.14.0") (source (origin (method url-fetch) - (uri (string-append - "http://bioconductor.org/packages/release/data/experiment" - "/src/contrib/pasilla_" version ".tar.gz")) + (uri (bioconductor-uri "pasilla" version 'experiment)) (sha256 (base32 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) @@ -1966,6 +1984,33 @@ closely reconstructs the mutational profile.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on Bioconductor packages. +(define-public r-jetset + (package + (name "r-jetset") + (version "3.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "jetset" version)) + (sha256 + (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp")))) + (properties `((upstream-name . "jetset"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi r-org-hs-eg-db)) + (home-page "http://www.cbs.dtu.dk/biotools/jetset/") + (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays") + (description + "This package provides a one-to-one mapping from gene to \"best\" probe +set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a, +hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single +gene may be measured by multiple probe sets. This can present a mild +conundrum when attempting to evaluate a gene \"signature\" that is defined by +gene names rather than by specific probe sets. This package also includes the +pre-calculated probe set quality scores that were used to define the +mapping.") + (license license:artistic2.0))) + +;; This is a CRAN package, but it depends on Bioconductor packages. (define-public r-nmf (package (name "r-nmf") @@ -2474,13 +2519,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.28.1") + (version "1.28.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "04s6y7q9dvg26fazs6lzkm668zpl3136j9gd5hkyihyrf4a1w3g3")))) + "0lkp7m2l66zq8yl788mkvi9kpb1haywxpf6ip9xl5y6iwm1w2b8p")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -2659,13 +2704,13 @@ analysis.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.30.2") + (version "1.30.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "1nr5p1h9131rvbpnh2kizzx9q6f4ycq6rzxy1yqg2pczqcg7hy4x")))) + "1f9m1p1viiigkmv15r2mknjrfw047jw1fylpqz5ipigc3jrphj1g")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3266,13 +3311,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.46.1") + (version "1.46.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1dm049r7k41m8zzp5b332fw3ah3jpzzgpcb21icxwhlg483ipjyv")))) + "0a3shdzc1r0f12q9w679hgj8ywrwbg36z7k0yp47dgfjl14lachk")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -4472,6 +4517,56 @@ this package. It also provides functionalities for visualizing, summarizing and comparing the clusterings.") (license license:expat))) +(define-public r-transcriptr + (package + (name "r-transcriptr") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "transcriptR" version)) + (sha256 + (base32 "1p5l2z3szx3qh02x7r81ajl7yc5wqsri6q6pzw83livmalcli5yy")))) + (properties `((upstream-name . "transcriptR"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-caret + r-chipseq + r-e1071 + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-proc + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/transcriptR") + (synopsis "Primary transcripts detection and quantification") + (description + "The differences in the RNA types being sequenced have an impact on the +resulting sequencing profiles. mRNA-seq data is enriched with reads derived +from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial +broader coverage of both exonic and intronic regions. The presence of +intronic reads in GRO-seq type of data makes it possible to use it to +computationally identify and quantify all de novo continuous regions of +transcription distributed across the genome. This type of data, however, is +more challenging to interpret and less common practice compared to mRNA-seq. +One of the challenges for primary transcript detection concerns the +simultaneous transcription of closely spaced genes, which needs to be properly +divided into individually transcribed units. The R package transcriptR +combines RNA-seq data with ChIP-seq data of histone modifications that mark +active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to +overcome this challenge. The advantage of this approach over the use of, for +example, gene annotations is that this approach is data driven and therefore +able to deal also with novel and case specific events.") + (license license:gpl3))) + (define-public r-trajectoryutils (package (name "r-trajectoryutils") @@ -4567,13 +4662,13 @@ that integrates the various evidences.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "1pw7d39944dwk5gw6q7igcn866zpqwz01ljaha2ih5dfvmhxka8n")))) + (base32 "009l27kb9gvwwf57dwxfribhfhvn4z5pw8yc847l6pkbzqggx678")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -4669,14 +4764,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "2.0.1") + (version "2.0.5") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1r0qc1pyff9nvjix21xjd6fmka06ywr4ipr8szm52hq41hwaiqgq")))) + "1j91pyfjsqngxxlxjqc477pznlfax4vayrks2q12rxw76ija80hf")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -4766,6 +4861,39 @@ provided as a matrix which can be used as an offset for different expression of gene-level counts.") (license license:gpl2+))) +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-valr + (package + (name "r-valr") + (version "0.6.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "valr" version)) + (sha256 + (base32 + "0dd41irvibh6rwi52bw4zg4m7wpyihlp1kdkb8fdji3csw2fiz4k")))) + (build-system r-build-system) + (propagated-inputs + (list r-broom + r-dplyr + r-ggplot2 + r-rcpp + r-readr + r-rlang + r-rtracklayer ;bioconductor package + r-stringr + r-tibble)) + (native-inputs + (list r-knitr)) + (home-page "https://github.com/rnabioco/valr") + (synopsis "Genome interval arithmetic in R") + (description + "This package enables you to read and manipulate genome intervals and +signals. It provides functionality similar to command-line tool suites within +R, enabling interactive analysis and visualization of genome-scale data.") + (license license:expat))) + (define-public r-variantannotation (package (name "r-variantannotation") @@ -5191,14 +5319,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.4.0") + (version "3.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "15p4jd9k520va6kzizkgsl4a18kh5r8i50qfdkv7xazsfhvxjm3i")))) + "1bz03ls7pkb09p6nkz7gfnhjlh06mgbp3j98ppnzibiar3cjrnfj")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -6212,14 +6340,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.4.0") + (version "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2")))) + "01662p5j9l12ylf5a5djg4cjppd2n3chrygzw8nnrcf1806xn58y")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -6554,14 +6682,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.22.1") + (version "1.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "05j3h314l2bw8n61h1nyiqhm3z7c1axycn4p3xkfccq5i4mcqvn2")))) + "1ln8l2cp6dqg6zv7s0qnmw5ii93v5sgp0b1nwswl52zdd8mivwxy")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -6798,6 +6926,7 @@ several functions from the R igraph package.") (uri (git-reference (url "https://github.com/pneuvial/sanssouci.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk")))) @@ -7743,14 +7872,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.2.0") + (version "4.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "18y7482sw0awlhazikq13r2r0zid9ksk942rma87m448y1cq2fi5")))) + "08jhcbanz24x7zdkxznxz787g0nk3jfzd7zsap13sra7qnwaswq4")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -8719,14 +8848,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.19.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "0fgcbskz96p5815nywsnqv2gzn7g93m438hpd5rpg85srg4wrpdj")))) + "08r05fzpraggbxv15lx0b68kjlkysp0rcdlm6n9avzmlsdqplb2h")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -8748,7 +8877,7 @@ decomposition algorithms.") r-keggrest r-limsolve r-magrittr - r-pmcmr + r-pmcmrplus r-pracma r-reshape2 r-somaticsignatures @@ -9375,6 +9504,7 @@ Gaussian distributions.") "0ardmryx6ac7v6n900a1klrrldvbmh7bxvy8ldz8rwid19h29ikr")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) + (inputs (list zlib)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Rbowtie/") @@ -9826,14 +9956,14 @@ cluster count and membership by stability evidence in unsupervised analysis.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.6.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "01r5dfjil1i526kb5gj9c8x9agi90x0bh7lzykbpn0g6s2hznbzi")))) + "16m5w6cp28p4fs2p8c8rjcg1d686xl8mpas816i7zxfh8m0bcqc9")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs @@ -10849,6 +10979,8 @@ with multiple R processes supported by the package @code{parallel}.") r-methylumi r-minfi r-watermelon)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/bigmelon/") (synopsis "Illumina methylation array analysis for large experiments") (description @@ -11237,14 +11369,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "0d6zrwbc4i2npl29idm1icwa62wdx47z9s8yx7k662v3qagwpj16")))) + "1p9zdrsxqn4ayvbj05xgpzpbzkzrh7k0d62x10069687vfl6dlxg")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -11287,14 +11419,14 @@ motifs, and others.") (define-public r-activedriverwgs (package (name "r-activedriverwgs") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "ActiveDriverWGS" version)) (sha256 (base32 - "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say")))) + "13b5yazgv9kckcp6gck183mh1m0q8lc5ixagmcy9s8kv2wz7wq45")))) (properties `((upstream-name . "ActiveDriverWGS"))) (build-system r-build-system) @@ -11302,6 +11434,9 @@ motifs, and others.") (list r-biostrings r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 + r-bsgenome-hsapiens-ucsc-hg38 + r-bsgenome-mmusculus-ucsc-mm9 + r-bsgenome-mmusculus-ucsc-mm10 r-genomeinfodb r-genomicranges r-iranges @@ -11322,14 +11457,14 @@ using whole genome sequencing data.") (define-public r-activepathways (package (name "r-activepathways") - (version "1.0.2") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "ActivePathways" version)) (sha256 (base32 - "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l")))) + "1prhwx0nnwy2q62l2r0z31mhk4mq6xdr6mjihdlwpwgwq4rfi60y")))) (properties `((upstream-name . "ActivePathways"))) (build-system r-build-system) @@ -11720,14 +11855,14 @@ searching and clustering.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.32.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "1nfp1alva6qim5rbhg9j9w97p2n4z21ghr4j489lqklkcs4d030f")))) + "0pa8d7p9asp36wddkg779i3b9m12rxik56c54bmclnammr0cz89i")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -13858,19 +13993,21 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "2.5-0") + (version "2.6-0") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw")))) + "0fr5pyc43hly5ry5bbygibbh9mnql7vl4r5qz42d0ry4hahyxa4w")))) (build-system r-build-system) (inputs (list gsl)) (propagated-inputs - (list r-lme4 + (list r-doparallel + r-foreach + r-lme4 r-nnet r-rcpp r-rcpparmadillo @@ -14045,13 +14182,13 @@ starting site, start codon, stop codon and transcription ending site.") (define-public r-sushi (package (name "r-sushi") - (version "1.31.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "1cj4palsq99vnwihp6z9mw0f8w9qj2vq8zwnabf3bgg0l1wpsc7c")))) + "073mh1d063ph5zk1d8kipgblr4l1ixqbxflhq4669761fi2frlw4")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs @@ -14445,14 +14582,14 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "1z4adapsnpw6fwanihdz43r11ijypxs5wbndb1i98j8kb7wf308k")))) + "0b5zva16r4kz8736h3djjgmh35nxmlin4f374rb4i2s55zsrb638")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs @@ -15006,13 +15143,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.22.1") + (version "2.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "0114pwbxg6mdhv94g556krl08ig7nwaafrryxbjha4hvn0xwy36l")))) + (base32 "0l7hfwgd8aiqv2k98jchkr3sdp9hwdg7pzm3bnvr6k7p93ifr6wc")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs @@ -15061,14 +15198,14 @@ starburst plots) in order to easily develop complete analysis pipelines.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.12.3") + (version "1.12.4") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "15l1jvfis7xzxwwnlqs8xpaf212v1lx513np2dc4l4h7rqhclm2v")))) + "1lm2r64d6sdfzvxcabgs0214cdc5dl9pfx562acjcxz5mb101g9g")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs |