diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 347 |
1 files changed, 314 insertions, 33 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f1af34844f..89b191585b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> -;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; ;;; This file is part of GNU Guix. @@ -1796,14 +1796,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.0.8") + (version "3.0.13") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "11svdfjp4faswrmzwkryzhd0ji2pl9vwsd35lvbfjgakbpxnyn8a")))) + "0kxn59v93hl5pq8d156lnbz0sslpnxyjcfrvq2gzgd91sd587qmn")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -2062,13 +2062,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1a3sw79185d6rld3wlrynkzcbp754a7jkracrmvn0ra964ia8zvc")))) + "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -4013,14 +4013,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0h0455plh8bxnpizgfxij9625ff32rs1a51yzpnrf5hl27xbfkdd")))) + "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) @@ -4049,14 +4049,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "3.18.0") + (version "3.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "07xkc515gp9j4axg0qh39ni65mcbjgxmzjh5wxd86w64lz7xh8b9")))) + "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -5877,14 +5877,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "025gfgn83ancp0khdmq2y4lwm97v5zqnjksi79rr0w175syznx5w")))) + "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs @@ -6103,14 +6103,14 @@ cluster count and membership by stability evidence in unsupervised analysis.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "1wylzps7wbvm64k62w5bbi8l74gaqca96psfapxfg6mcac5yz4qw")))) + "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (arguments @@ -6810,6 +6810,59 @@ accessibility data.") ,@(alist-delete "r-monocle" (package-propagated-inputs r-cicero))))))) +(define-public r-circrnaprofiler + (package + (name "r-circrnaprofiler") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "circRNAprofiler" version)) + (sha256 + (base32 + "1rwpl9a5p5242aiapik0vf4ywqh7m6phzl8z8qmzcy0imbx7mpbn")))) + (properties + `((upstream-name . "circRNAprofiler"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-deseq2" ,r-deseq2) + ("r-dplyr" ,r-dplyr) + ("r-edger" ,r-edger) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-gwascat" ,r-gwascat) + ("r-iranges" ,r-iranges) + ("r-magrittr" ,r-magrittr) + ("r-r-utils" ,r-r-utils) + ("r-readr" ,r-readr) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-seqinr" ,r-seqinr) + ("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr) + ("r-universalmotif" ,r-universalmotif))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/Aufiero/circRNAprofiler") + (synopsis + "Computational framework for the downstream analysis of circular RNA's") + (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 +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")) @@ -6965,14 +7018,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "0x8ik179sf38ihx2y24cvsa9d8isdmx2z27sjhcwq0r3xpjxpz1a")) + "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -7435,6 +7488,56 @@ data. This modified test allows for testing differential expression in qPCR data.") (license license:gpl2+))) +(define-public r-universalmotif + (package + (name "r-universalmotif") + (version "1.8.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "universalmotif" version)) + (sha256 + (base32 + "1ys2kbayc1rzv8nzi60208yfslm4kzynndfg7vw2n0c30dvzycrc")))) + (properties + `((upstream-name . "universalmotif"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-reference-to-strip + (lambda _ + (substitute* "src/Makevars" + (("/usr/bin/strip") (which "strip")))))))) + (propagated-inputs + `(("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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://bioconductor.org/packages/universalmotif/") + (synopsis + "Specific structures importer, modifier, and exporter for R") + (description + "This package allows importing most common @dfn{specific structure} +(motif) types into R for use by functions provided by other Bioconductor +motif-related packages. Motifs can be exported into most major motif formats +from various classes as defined by other Bioconductor packages. A suite of +motif and sequence manipulation and analysis functions are included, including +enrichment, comparison, P-value calculation, shuffling, trimming, higher-order +motifs, and others.") + (license license:gpl3))) + ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activedriverwgs @@ -7812,14 +7915,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.42.0") + (version "3.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "14q9zhhxgkx5skj424i2rbjdbp5j8jfkxspkhnkwv5i45cvkgh19")))) + "1853w19042c53whdnrfg1v8f07wpswf2si8q4613yrcamzg2zjkx")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -8574,14 +8677,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.52.0") + (version "1.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1i5ky3bfbkrz4lgfs72fkckr8q3wq48p38mp05cjmnmh1chmdw38")))) + "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -8728,14 +8831,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1hr149q03p09y1cjnx8av854j53041wfyq66xpsjw4mypzjf6f28")))) + "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (arguments @@ -8769,14 +8872,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0wia85a6dkgibsjcmpqas5068msck3h3bqpgw2x07bk189z4vay2")) + "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28")) (modules '((guix build utils))) (snippet '(begin @@ -8853,14 +8956,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.6.2") + (version "2.6.4") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "1yxm5andf4hsxxsmwrn5vl79707yfqkhzzajq6fvhsmaad3f97n7")))) + "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8875,6 +8978,184 @@ variety of commonly used matrix types, including sparse and HDF5-backed matrices.") (license license:gpl3))) +;; This package includes files that have been taken from kentutils. Some +;; parts of kentutils are not released under a free license, but this package +;; only uses files that are also found in the free parts of kentutils. +(define-public r-cner + (package + (name "r-cner") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CNEr" version)) + (sha256 + (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c")))) + (properties `((upstream-name . "CNEr"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-go-db" ,r-go-db) + ("r-iranges" ,r-iranges) + ("r-keggrest" ,r-keggrest) + ("r-powerlaw" ,r-powerlaw) + ("r-r-utils" ,r-r-utils) + ("r-readr" ,r-readr) + ("r-reshape2" ,r-reshape2) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/ge11232002/CNEr") + (synopsis "CNE Detection and Visualization") + (description + "This package provides tools for large-scale identification and +advanced visualization of sets of conserved noncoding elements.") + ;; For all files in src/ucsc "license is hereby granted for all use - + ;; public, private or commercial"; this includes those files that don't + ;; have a license header, because they are included in the free parts of + ;; the kentutils package. + (license (list license:gpl2 + (license:non-copyleft + "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE"))))) + +(define-public r-tfbstools + (package + (name "r-tfbstools") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TFBSTools" version)) + (sha256 + (base32 + "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha")))) + (properties `((upstream-name . "TFBSTools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-catools" ,r-catools) + ("r-cner" ,r-cner) + ("r-dbi" ,r-dbi) + ("r-dirichletmultinomial" ,r-dirichletmultinomial) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-seqlogo" ,r-seqlogo) + ("r-tfmpvalue" ,r-tfmpvalue) + ("r-xml" ,r-xml) + ("r-xvector" ,r-xvector))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/ge11232002/TFBSTools") + (synopsis "Transcription factor binding site (TFBS) analysis") + (description + "TFBSTools is a package for the analysis and manipulation of +transcription factor binding sites. It includes matrices conversion +between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight +Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also +scan putative TFBS from sequence/alignment, query JASPAR database and +provides a wrapper of de novo motif discovery software.") + (license license:gpl2))) + +(define-public r-motifmatchr + (package + (name "r-motifmatchr") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "motifmatchr" version)) + (sha256 + (base32 + "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z")))) + (properties `((upstream-name . "motifmatchr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tfbstools" ,r-tfbstools))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/motifmatchr") + (synopsis "Fast motif matching in R") + (description + "Quickly find motif matches for many motifs and many sequences. +This package wraps C++ code from the MOODS motif calling library.") + (license license:gpl3))) + +(define-public r-chromvar + (package + (name "r-chromvar") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "chromVAR" version)) + (sha256 + (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819")))) + (properties `((upstream-name . "chromVAR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-dt" ,r-dt) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-miniui" ,r-miniui) + ("r-nabor" ,r-nabor) + ("r-plotly" ,r-plotly) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rsamtools" ,r-rsamtools) + ("r-rtsne" ,r-rtsne) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tfbstools" ,r-tfbstools))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html") + (synopsis "Determine chromatin variation across regions") + (description + "This package @code{r-chromvar} determines variation in chromatin +accessibility across sets of annotations or peaks. @code{r-chromvar} is +designed primarily for single-cell or sparse chromatin accessibility data like +single cell assay for transposase-accessible chromatin using +sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease +sequence (@code{DNAse-seq}) experiments.") + (license license:expat))) + (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") @@ -8907,14 +9188,14 @@ libraries.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "0l2r6fhyd33dllf2mc5a1pd5sawfvcin54pgh9l1nafqzg3sdv2m")))) + "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -8979,14 +9260,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.18.1") + (version "1.18.5") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1zap12rm61z2hg6ykknbif478nr7g468v8mp50bj5hqgi69ywcww")))) + "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -9022,14 +9303,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0d1idbda1pzhdam9m0i5rn0c6pl7gwv0v3mcrv4wi5760v9qd5qh")))) + "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) @@ -9050,14 +9331,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.12.1") + (version "1.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1cyvj6ffl10vaiip146dldc1w8if854kpz9nhi50ndhpkmdb8sa0")))) + "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) |