diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 104 |
1 files changed, 86 insertions, 18 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6e0c5a1e6..e004560d58 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -722,6 +722,49 @@ 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 +1569,30 @@ 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") @@ -1867,14 +1934,14 @@ 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 +2095,14 @@ 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 @@ -2156,14 +2223,14 @@ 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 @@ -3284,14 +3351,14 @@ 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 @@ -3942,14 +4009,14 @@ 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 +5372,14 @@ 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 +5884,14 @@ 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 +5926,14 @@ 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 +6004,14 @@ 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 "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0mmm7vvzq50b5fayid0bw82b5lar3xm9fwl2ya30q0p4db2y6wnz")))) + "07g6r335zqqy3r5v4x4glxdrcsq9bjhs9jmgvppiggv1h630a22w")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -5966,6 +6033,7 @@ 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") |