diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 162 |
1 files changed, 101 insertions, 61 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e8d353f49a..a284ea8d41 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2034,14 +2034,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.0.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "1p9773fv7j7q4x1sjqqaw32qy9lqn2gf6gkynh1d8n1kd7v7sclp")))) + "12i8lafy1z97gs4knqi7r5l1hd7dr6j8a23qj4fkdpqsdpyz21z7")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -2154,13 +2154,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.48.1") + (version "2.48.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1a1lh0z1vk1q3wil85pi7v0f9miv070sjkbnwbw390zvncwakqxa")))) + "1na271z9gc3b7xfcghbljj9lqq6v9b2kb71xahsq544yv4z9w8xj")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -2192,13 +2192,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "17w4gdajxxmsfgiwycp1d7rbxdqhc5jnngcb58ky0fv5xbv9f4j0")))) + "1jx1wm47s64ywfddrg8kqzz4xpcmfjwrzbxhvlmys7pf2hzj4gbh")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -2675,14 +2675,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-edaseq (package (name "r-edaseq") - (version "2.26.0") + (version "2.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "1mqpi2iz4azr31b3ajsqb4n9izjh85dx642844n059c8s2pfmivh")))) + "0pakcbkalhhqz3d9lpfx3hscf53k24mlmrywxxzfg43yq57srkql")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -2743,14 +2743,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.16.0") + (version "2.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "100m2mzxl4pmldqixzfdznnd4nqbykk2l7n4xazqjpnlpcldy2dj")))) + "0mbdfxic2vkfwm6b16353zr0qg8ylwf1vrxry85j2lgzl1qyyras")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -2944,13 +2944,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0wjd7sh7kr9lfcdbzm5jdynl84nfsl7nqvly92qqrdcxd2sjfr63")))) + "1ga8yrn7j1wn9wdsvf4ws6n2987yk1yxz22v2jzaszfikhjh1sp8")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -3300,13 +3300,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-limma (package (name "r-limma") - (version "3.48.0") + (version "3.48.1") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1mkpl2b1ksylc6dih4a6kgjjia8advikzmqmv762j4r7gya950pf")))) + "1wscxvhrz16sfa0qwk9anxqjy1vgvqmq6ia9gx6pwpga8qzwn5bi")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -3571,14 +3571,14 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.26.0") + (version "2.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1m5xvnv0rxyrfri4jwyyryr13d55nyhqvfc5xxg5mpskw2v029kp")) + "0z4cz6lir9gwzy0hxwv03wv36fkkfdb97p9wv4af020k0zkp3ipr")) (modules '((guix build utils))) (snippet '(begin @@ -3601,7 +3601,7 @@ specific parser.") #t))))) (inputs `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.26.0. + ;; mzR version 2.26.1. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs @@ -4319,14 +4319,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.26.2") + (version "1.26.3") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1apqi5ih06s37v7wpp13ybksiinrwj0ii6mx6vvvfkb6ix0wljws")))) + "01l35l5zj87qkarrbal9la6kshk3j7k8hy3iimv3gdnnz4axmvs7")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -4334,6 +4334,7 @@ unmodeled, or latent sources of noise.") ("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) @@ -4349,6 +4350,7 @@ unmodeled, or latent sources of noise.") ("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) @@ -4765,14 +4767,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.2.2") + (version "3.2.4") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "037z4mm8q5c50lwf63l1gmksd9fzfmyyp259jncpsxa3almf5jgh")))) + "024ff12v42yvcma29cis4f777jrdgmgfr06lxn6l3nh30ghxawci")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -7240,14 +7242,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.18.0") + (version "3.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "1x9cg6qlvbcdb965jh01w07ibc4lj30ikq1v312rdih3sn6zsdck")))) + "1g3llrb51m8lj3prcr6ryxj0lf4qqzg9mzi36y71pp9qzfvf3c0k")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -7275,14 +7277,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "116mwmpr06f4z60avdsfzdalbxn4119dbzk3jz1q5fp81qvw164d")))) + "194sfmcnjfi3fvvfpljg1f80f44vvvxiij336b8z1dgzki6bqa3r")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) @@ -7312,14 +7314,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.0.0") + (version "4.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "1lmrb6ddpx1p3kdrwszhxq6nndmbiqipzrclk64mnp63y7g50q56")))) + "11pjzh7inh1x0gry42nlq4har65s8pc0w3bkccm6kmxycvaxb9rh")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -7437,14 +7439,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.63.1") + (version "1.64.2") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "071qr68dn8k3mvwgpllbk2a4g6f6yyv2087q5rmpb22lkfvi4hwv")))) + "03y633vgxprd2abhanj4sanmb4ymz7az5aiasxn6wjzawiqjdcb1")))) (build-system r-build-system) (arguments `(#:phases @@ -9368,14 +9370,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.6.1") + (version "2.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "007pbvxkhh930zdkgjaihannjbpbfnbizp3ffc2vyxygw0r4vz68")))) + "04nz85vr184fjmf2k0kc5sy2hjzpfazfkxlhlgax50rnkn98va5x")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -9930,14 +9932,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.16.0") + (version "6.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "1hri5rrqf8vq3c6pivfamv60yz9mf9rrdpdd5bw2h24lghm2x8rw")))) + "0fiwf86hvkidxwkdcw0x7lk3bk2fsxqng43b1js7klifm3gfcf91")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -10208,11 +10210,56 @@ 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) @@ -10222,13 +10269,13 @@ 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) @@ -10239,17 +10286,10 @@ 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 @@ -11528,13 +11568,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.20.1") + (version "2.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "0gkprmilj6lwnyghpyfzkwmfl3gva75lgpn4ck8jgikqac8jcq0x")))) + "0p2wdq5vrx63ndghl9ww428z2lwnv5y88xmcr51by2g6vcj3brcf")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -11680,14 +11720,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "0y396lx2mh9izb07lz83j35wydfj808ihc74jlgras03a3g335p2")))) + "1ix09a39z7y2cj0y8qsd66ka8a8y8q79w08l4jv1yhhn9h4va89s")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs @@ -12346,14 +12386,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.14.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0ld1p3rxsx47bdq2wz9110zvwhabsnn92wkhz8x7xzfr01cc9glm")) + "1cwynbcaaxmbh45fc0d264liqdj0wbjlj7k2bsq3qfjbnh6kkam5")) (modules '((guix build utils))) (snippet '(begin @@ -12970,14 +13010,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "1lzi3wylx94k3gmfw5lsqh3cvg485ik3n5xd51jllczgavwvki16")))) + "12frw4myqr8y3ff4n74ld4478ndpmfj5ynr6gnigbr1h61b94m3v")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -13236,14 +13276,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.36.1") + (version "1.36.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "1mljj70pg36dgrqhdfj643p39wbps66zz23xw6km150lq6fpgpg5")))) + "0lp0k8jd4dfsfn10706124graaqnzcyv1siblvm8dn2ykw2rc6vl")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs |