diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 321 |
1 files changed, 275 insertions, 46 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7e993189d6..e7f11dead3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -201,14 +201,14 @@ genomes and gene ID formats, largely based on the UCSC table browser.") (define-public r-hpar (package (name "r-hpar") - (version "1.22.2") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388")))) + "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") @@ -219,23 +219,24 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb")))) + "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs - `(("r-memoise" ,r-memoise) - ("r-genomicranges" ,r-genomicranges) + `(("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) - ("r-rtracklayer" ,r-rtracklayer) ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-memoise" ,r-memoise) + ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") @@ -247,14 +248,14 @@ region sets and other genomic features.") (define-public r-diffbind (package (name "r-diffbind") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish")))) + "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (inputs @@ -292,14 +293,14 @@ occupancy (overlap) analysis and plotting functions.") (define-public r-ripseeker (package (name "r-ripseeker") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 - "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi")))) + "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i")))) (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs @@ -325,14 +326,14 @@ processing to visualization and annotation.") (define-public r-multtest (package (name "r-multtest") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0")))) + "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) @@ -360,21 +361,69 @@ cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.") (license license:lgpl3))) +(define-public r-graph + (package + (name "r-graph") + (version "1.60.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "graph" version)) + (sha256 + (base32 + "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "https://bioconductor.org/packages/graph") + (synopsis "Handle graph data structures in R") + (description + "This package implements some simple graph handling capabilities for R.") + (license license:artistic2.0))) + +(define-public r-codedepends + (package + (name "r-codedepends") + (version "0.6.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "CodeDepends" version)) + (sha256 + (base32 + "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) + (properties `((upstream-name . "CodeDepends"))) + (build-system r-build-system) + (propagated-inputs + `(("r-codetools" ,r-codetools) + ("r-graph" ,r-graph) + ("r-xml" ,r-xml))) + (home-page "http://cran.r-project.org/web/packages/CodeDepends") + (synopsis "Analysis of R code for reproducible research and code comprehension") + (description + "This package provides tools for analyzing R expressions or blocks of +code and determining the dependencies between them. It focuses on R scripts, +but can be used on the bodies of functions. There are many facilities +including the ability to summarize or get a high-level view of code, +determining dependencies between variables, code improvement suggestions.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.14.0") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0")))) + "09fhh1355diip3v3c0skmp1336vclipkm5nv02qvp5902v4262y3")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) ("r-biostrings" ,r-biostrings) ("r-delayedarray" ,r-delayedarray) ("r-go-db" ,r-go-db) @@ -390,7 +439,6 @@ expressed genes in DNA microarray experiments.") ("r-multtest" ,r-multtest) ("r-rbgl" ,r-rbgl) ("r-graph" ,r-graph) - ("r-biocinstaller" ,r-biocinstaller) ("r-regioner" ,r-regioner) ("r-dbi" ,r-dbi) ("r-ensembldb" ,r-ensembldb) @@ -418,12 +466,12 @@ enrichedGO (addGeneIDs).") (define-public r-marray (package (name "r-marray") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d")))) + (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) @@ -437,12 +485,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq")))) + (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -457,12 +505,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz")))) + (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -480,12 +528,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd")))) + (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -512,14 +560,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg")))) + "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -538,14 +586,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs")))) + "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -572,14 +620,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0")))) + "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -611,14 +659,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn")))) + "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -639,14 +687,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n")))) + "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -671,14 +719,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q")))) + "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -710,14 +758,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9")))) + "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") @@ -730,14 +778,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l")))) + "1401x0jn5f8hqc12r3gd1wammp1nxir3is1k5ldd03ln97x00i7a")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -756,14 +804,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "1.8.2") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s")))) + "0cbsi6g8k1whkh21jxfn22sj7wry2g3rshiracf5nyvrl2fnl947")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs @@ -783,14 +831,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3")))) + "137c06g5w7mjw3b1mly7b7n9iix4fcy23c7a9ym9iz8dazwhzwn5")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -807,14 +855,14 @@ in omics data.") (define-public r-inspect (package (name "r-inspect") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "1gk0pwyimkswrvgb2xr3c2zy4myi448a2shr5ap65rq9pcpp0l8p")))) + "0b671x5v2wyq5np2flq2m1fnjz32f303yjlw64a1inwc9k2w2pz2")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -839,3 +887,184 @@ Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and assess via modeling the rates that determines changes in mature mRNA levels.") (license license:gpl2))) + +(define-public r-dnabarcodes + (package + (name "r-dnabarcodes") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DNABarcodes" version)) + (sha256 + (base32 + "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0")))) + (properties `((upstream-name . "DNABarcodes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp))) + (home-page "https://bioconductor.org/packages/DNABarcodes") + (synopsis "Create and analyze DNA barcodes") + (description + "This package offers tools to create DNA barcode sets capable of +correcting insertion, deletion, and substitution errors. Existing barcodes +can be analyzed regarding their minimal, maximal and average distances between +barcodes. Finally, reads that start with a (possibly mutated) barcode can be +demultiplexed, i.e. assigned to their original reference barcode.") + (license license:gpl2))) + +(define-public r-ruvseq + (package + (name "r-ruvseq") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RUVSeq" version)) + (sha256 + (base32 + "0xb3bj3n06cb9xddkv77a8svhg4fl1azlfmibwrm9mq9464kgf0m")))) + (properties `((upstream-name . "RUVSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-edaseq" ,r-edaseq) + ("r-edger" ,r-edger) + ("r-mass" ,r-mass))) + (home-page "https://github.com/drisso/RUVSeq") + (synopsis "Remove unwanted variation from RNA-Seq data") + (description + "This package implements methods to @dfn{remove unwanted variation} (RUV) +of Risso et al. (2014) for the normalization of RNA-Seq read counts between +samples.") + (license license:artistic2.0))) + +(define-public r-biocneighbors + (package + (name "r-biocneighbors") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocNeighbors" version)) + (sha256 + (base32 + "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll")))) + (properties `((upstream-name . "BiocNeighbors"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-rcpp" ,r-rcpp) + ("r-rcppannoy" ,r-rcppannoy) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/BiocNeighbors") + (synopsis "Nearest Neighbor Detection for Bioconductor packages") + (description + "This package implements exact and approximate methods for nearest +neighbor detection, in a framework that allows them to be easily switched +within Bioconductor packages or workflows. The exact algorithm is implemented +using pre-clustering with the k-means algorithm. Functions are also provided +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-destiny + (package + (name "r-destiny") + (version "2.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "destiny" version)) + (sha256 + (base32 + "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-fnn" ,r-fnn) + ("r-ggthemes" ,r-ggthemes) + ("r-hmisc" ,r-hmisc) + ("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix) + ("r-proxy" ,r-proxy) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-scales" ,r-scales) + ("r-scatterplot3d" ,r-scatterplot3d) + ("r-smoother" ,r-smoother) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-vim" ,r-vim))) + (home-page "https://bioconductor.org/packages/destiny/") + (synopsis "Create and plot diffusion maps") + (description "This package provides tools to create and plot diffusion +maps.") + ;; Any version of the GPL + (license license:gpl3+))) + +(define-public r-savr + (package + (name "r-savr") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "savR" version)) + (sha256 + (base32 + "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7")))) + (properties `((upstream-name . "savR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) + ("r-xml" ,r-xml))) + (home-page "https://github.com/bcalder/savR") + (synopsis "Parse and analyze Illumina SAV files") + (description + "This package provides tools to parse Illumina Sequence Analysis +Viewer (SAV) files, access data, and generate QC plots.") + (license license:agpl3+))) + +(define-public r-chipexoqual + (package + (name "r-chipexoqual") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ChIPexoQual" version)) + (sha256 + (base32 + "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp")))) + (properties `((upstream-name . "ChIPexoQual"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-biovizbase" ,r-biovizbase) + ("r-broom" ,r-broom) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-hexbin" ,r-hexbin) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rmarkdown" ,r-rmarkdown) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-viridis" ,r-viridis))) + (home-page "https://github.com/keleslab/ChIPexoQual") + (synopsis "Quality control pipeline for ChIP-exo/nexus data") + (description + "This package provides a quality control pipeline for ChIP-exo/nexus +sequencing data.") + (license license:gpl2+))) |