diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 88 |
1 files changed, 65 insertions, 23 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 76ff773ef1..ed35b4c61a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2018 Roel Janssen <roel@gnu.org> +;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -28,17 +29,49 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages bioinformatics)) +(define-public r-bsgenome-dmelanogaster-ucsc-dm6 + (package + (name "r-bsgenome-dmelanogaster-ucsc-dm6") + (version "1.4.1") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "BSgenome.Dmelanogaster.UCSC.dm6_" + version ".tar.gz")) + (sha256 + (base32 + "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) + (properties + `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) + (build-system r-build-system) + ;; As this package provides little more than a very large data file it + ;; doesn't make sense to build substitutes. + (arguments `(#:substitutable? #f)) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome))) + (home-page + "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") + (synopsis "Full genome sequences for Fly") + (description + "This package provides full genome sequences for Drosophila +melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings +objects.") + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") - (version "1.20.0") + (version "1.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "0s5v79mgxdx862v1jrdf5pdap81nz5vjx25ni8s3sl97ldckf6j8")))) + "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") @@ -49,14 +82,14 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp")))) + "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -65,7 +98,8 @@ the Human Protein Atlas project.") ("r-bsgenome" ,r-bsgenome) ("r-rtracklayer" ,r-rtracklayer) ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges))) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") (description "This package offers a statistical framework based on @@ -76,14 +110,14 @@ region sets and other genomic features.") (define-public r-diffbind (package (name "r-diffbind") - (version "2.6.6") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1sm5h6nq77hjfis6kr1nqyizcxgfz87dgpqc4fxlfqkmsd9n3vkp")))) + "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (inputs @@ -95,6 +129,8 @@ region sets and other genomic features.") ("r-dplyr" ,r-dplyr) ("r-edger" ,r-edger) ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-gplots" ,r-gplots) ("r-iranges" ,r-iranges) @@ -105,6 +141,7 @@ region sets and other genomic features.") ("r-rcpp" ,r-rcpp) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-systempiper" ,r-systempiper) ("r-zlibbioc" ,r-zlibbioc))) (home-page "http://bioconductor.org/packages/DiffBind") @@ -118,14 +155,14 @@ occupancy (overlap) analysis and plotting functions.") (define-public r-ripseeker (package (name "r-ripseeker") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 - "0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y")))) + "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi")))) (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs @@ -151,14 +188,14 @@ processing to visualization and annotation.") (define-public r-multtest (package (name "r-multtest") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "0n11rd49xl2vn3ldmfips7d3yb70l8npjcqsxyswr9ypjhgzkv9j")))) + "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) @@ -189,23 +226,27 @@ expressed genes in DNA microarray experiments.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.12.7") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1zab489d7a6bh6ylc68x6yn47gdkmr7p3677grx9l2qafrryjr04")))) + "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-delayedarray" ,r-delayedarray) ("r-go-db" ,r-go-db) ("r-biomart" ,r-biomart) ("r-bsgenome" ,r-bsgenome) ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) ("r-genomeinfodb" ,r-genomeinfodb) + ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats) ("r-annotationdbi" ,r-annotationdbi) ("r-limma" ,r-limma) @@ -217,6 +258,7 @@ expressed genes in DNA microarray experiments.") ("r-dbi" ,r-dbi) ("r-ensembldb" ,r-ensembldb) ("r-biobase" ,r-biobase) + ("r-s4vectors" ,r-s4vectors) ("r-seqinr" ,r-seqinr) ("r-idr" ,r-idr) ("r-genomicalignments" ,r-genomicalignments) @@ -239,16 +281,15 @@ enrichedGO (addGeneIDs).") (define-public r-marray (package (name "r-marray") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "14c93i86yc7jn4ax8p4l0z6v9xisw1bv7gzb4a0gbxhxn7mddaic")))) + (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limma" ,r-limma))) + `(("r-limma" ,r-limma))) (home-page "http://bioconductor.org/packages/marray") (synopsis "Exploratory analysis for two-color spotted microarray data") (description "This package contains class definitions for two-color spotted @@ -259,12 +300,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "0fynvcsjdbgp69i0nxrc8ni58rhb1kx9k5r3nb91n9i8s43gjqlm")))) + (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -279,12 +320,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "11pi6awz3858yb4s0z3qf3kcmsdgp6d4aj41g4lfix1sv5amllch")))) + (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -302,16 +343,17 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "0lgbv4s0xqgrs7q6ynb3c273sf7pyrp51jnc8ravq1z5g0a2zshy")))) + (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) + ("r-biocparallel" ,r-biocparallel) ("r-cghbase" ,r-cghbase) ("r-cghcall" ,r-cghcall) ("r-dnacopy" ,r-dnacopy) |