diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 161 |
1 files changed, 123 insertions, 38 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6e0c5a1e6..63687036fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -224,6 +224,30 @@ Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") (license license:artistic2.0))) +(define-public r-bsgenome-hsapiens-ncbi-grch38 + (package + (name "r-bsgenome-hsapiens-ncbi-grch38") + (version "1.3.1000") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38" + version 'annotation)) + (sha256 + (base32 + "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) + (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) + (build-system r-build-system) + (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) + (home-page + "https://bioconductor.org/packages/release/data/annotation/html/\ +BSgenome.Hsapiens.NCBI.GRCh38.html") + (synopsis "Full genome sequences for Homo sapiens (GRCh38)") + (description + "This package provides full genome sequences for Homo sapiens (Human) as +provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") + (license license:artistic2.0))) + (define-public r-bsgenome-hsapiens-ucsc-hg19-masked (package (name "r-bsgenome-hsapiens-ucsc-hg19-masked") @@ -594,14 +618,14 @@ database is exposed as a @code{TxDb} object.") (define-public r-txdb-mmusculus-ucsc-mm10-knowngene (package (name "r-txdb-mmusculus-ucsc-mm10-knowngene") - (version "3.4.7") + (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene" version 'annotation)) (sha256 (base32 - "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b")))) + "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9")))) (properties `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) (build-system r-build-system) @@ -722,6 +746,49 @@ the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.") (license license:gpl2+))) +;; This is a CRAN package, but it depends on Bioconductor packages. +(define-public r-nmf + (package + (name "r-nmf") + (version "0.22.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "NMF" version)) + (sha256 + (base32 + "0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq")))) + (properties `((upstream-name . "NMF"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-biobase" ,r-biobase) + ("r-biocmanager" ,r-biocmanager) + ("r-bigmemory" ,r-bigmemory) ; suggested + ("r-synchronicity" ,r-synchronicity) ; suggested + ("r-colorspace" ,r-colorspace) + ("r-digest" ,r-digest) + ("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-gridbase" ,r-gridbase) + ("r-pkgmaker" ,r-pkgmaker) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-registry" ,r-registry) + ("r-reshape2" ,r-reshape2) + ("r-rngtools" ,r-rngtools) + ("r-stringr" ,r-stringr))) + (home-page "http://renozao.github.io/NMF") + (synopsis "Algorithms and framework for nonnegative matrix factorization") + (description + "This package provides a framework to perform Non-negative Matrix +Factorization (NMF). The package implements a set of already published +algorithms and seeding methods, and provides a framework to test, develop and +plug new or custom algorithms. Most of the built-in algorithms have been +optimized in C++, and the main interface function provides an easy way of +performing parallel computations on multicore machines.") + (license license:gpl2+))) + (define-public r-do-db (package (name "r-do-db") @@ -1526,6 +1593,30 @@ expressed genes in DNA microarray experiments.") "This package implements some simple graph handling capabilities for R.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-ggm + (package + (name "r-ggm") + (version "2.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggm" version)) + (sha256 + (base32 + "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di")))) + (properties `((upstream-name . "ggm"))) + (build-system r-build-system) + (propagated-inputs + `(("r-graph" ,r-graph) + ("r-igraph" ,r-igraph))) + (home-page "https://cran.r-project.org/package=ggm") + (synopsis "Functions for graphical Markov models") + (description + "This package provides functions and datasets for maximum likelihood +fitting of some classes of graphical Markov models.") + (license license:gpl2+))) + (define-public r-codedepends (package (name "r-codedepends") @@ -1557,14 +1648,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.20.0") + (version "3.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0hp3s3shnrb55cxvx9wrdl67wqw9f55gdgx7262s4mahpxjswfsa")))) + "0kmfha4vprbi0z6n7v9w28xfrqcx5qad7yfr0b316j5aj8v9f4hc")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -1867,14 +1958,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "10kwb70c9aq0bfqpq48h186lsbwgrg18m14r9z8x6n8l7cds5azc")))) + "140bp7c8p079xh5wwxmrq3a73pm6mdc9czq5w2gzjml7dgrca38a")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -2028,14 +2119,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.16.2") + (version "1.16.3") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "1g8la7k4pnyr2hvk4yjd1bwvjy6nqbbb0fwxrrh2ifgqf4h21x2p")))) + "0y4gpvrbmcipdnyz9lz9ywn0317xnpcriiisqvxygin05vgcpilp")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -2125,14 +2216,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf")))) + "1bx7i5pifj8w89fnhfgcfgcar2ik2ad8wqs2rix7yks90vz185i6")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -2156,14 +2247,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "0fjfmmpda7pszsck2hm7bp4509pl3xaz02q2q03d5vla62h1h81k")))) + "1282fdwxrpga87y8xflr0sl8ajwawgn2i9i65my8mbg5vrixs407")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -3130,27 +3221,20 @@ surface of a flowcell.") (define-public r-gkmsvm (package (name "r-gkmsvm") - (version "0.79.0") + (version "0.80.0") (source (origin (method url-fetch) (uri (cran-uri "gkmSVM" version)) (sha256 (base32 - "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) + "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p")))) (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernlab" ,r-kernlab) + `(("r-kernlab" ,r-kernlab) ("r-rcpp" ,r-rcpp) ("r-rocr" ,r-rocr) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) ("r-seqinr" ,r-seqinr))) (home-page "https://cran.r-project.org/web/packages/gkmSVM") (synopsis "Gapped-kmer support vector machine") @@ -3284,14 +3368,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "2.32.0") + (version "2.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0hx5gqgh4xrkx37ccprq7azj9jziff137bdk0gvrixcx52ws6h89")))) + "1ldxj2hasg6ysh70sc73mz2v4h3n8gf3lii09c3sqc4wmz5h7rp1")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -3521,14 +3605,14 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.66.2") + (version "1.66.4") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "1wc280iw9vllg6f58vsdj895yaqs8w42kl7jk8sgii009gwlaj8d")))) + "19hlicdndy2p45y7w91gnwi3wgq5s465a646z3qqk8gmn5sn614q")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -3942,14 +4026,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "12ix0bvwk50d48z85f3453k7szm1j27gk4qgw56az4fxra472rlh")))) + "0dzrizacy3br8fiy1vnsl5zf242lg1hqv9dyv5ayqh2n480is57f")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -5305,14 +5389,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0l8q9y2a4m1di0w5nlxhq9jgliinhgr2fwjpm5ixnqx5j3iprlwd")))) + "0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -5817,14 +5901,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.10.6") + (version "6.10.8") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "18jwrdyc4pnx917y1kskxz3fqvlrkyy4ny0xqrfcidz0j7p0b7wr")))) + "0307vhx9ck24rxqbvq15815ssxcc226sl2la060n204b51wi9jaa")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -5859,14 +5943,14 @@ delete entire rows with missing data.") (define-public r-depecher (package (name "r-depecher") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "1f6zbc0fq7xjflh3mkjx1n83mpppw663dj22rlpxzwp1kpmf6wm5")))) + "08ja6ayvbax9m3x9w3xzi72z97miiha2nbsild1gp77n6sgn5i35")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs @@ -5937,14 +6021,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0mmm7vvzq50b5fayid0bw82b5lar3xm9fwl2ya30q0p4db2y6wnz")))) + "154djqd32w87814ycfmfz27ikp17bnampvmvw5hzi5p2x9l3h82r")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -5966,6 +6050,7 @@ genes in the gene-set that are ranked above the leading edge).") ("r-s4vectors" ,r-s4vectors) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) ("r-vgam" ,r-vgam))) (home-page "https://bioconductor.org/packages/cicero/") (synopsis "Predict cis-co-accessibility from single-cell data") @@ -7205,14 +7290,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.12.2") + (version "1.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "0722f3jl1xq8k8w7vrv986jd16bgysqp3n07pgmdn0hh1zh2mcqc")))) + "1vf6l88j3n6109j6sd08wfqxqpj2k20dvr8ll9zl1szsn18b4gny")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) |