diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 98 |
1 files changed, 71 insertions, 27 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 176f7ecc6d..1e87b190c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2188,6 +2188,50 @@ set analyses, and can deal with repeated or longitudinal data.") biological sequences.") (license license:gpl3))) +(define-public r-deconvr + (package + (name "r-deconvr") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "deconvR" version)) + (sha256 + (base32 + "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3")))) + (properties `((upstream-name . "deconvR"))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-biocgenerics + r-data-table + r-dplyr + r-e1071 + r-foreach + r-genomicranges + r-iranges + r-magrittr + r-mass + r-matrixstats + r-methylkit + r-nnls + r-quadprog + r-rsq + r-s4vectors + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/BIMSBbioinfo/deconvR") + (synopsis "Simulation and deconvolution of omic profiles") + (description + "This package provides a collection of functions designed for analyzing +deconvolution of the bulk sample(s) using an atlas of reference omic signature +profiles and a user-selected model. Users are given the option to create or +extend a reference atlas and,also simulate the desired size of the bulk +signature profile of the reference cell types. The package includes the +cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can +be used in deconvolution. Additionally, we included @code{BSmeth2Probe}, to +make mapping WGBS data to their probe IDs easier.") + (license license:artistic2.0))) + (define-public r-decoupler (package (name "r-decoupler") @@ -2232,13 +2276,13 @@ targeted by a kinase.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.42.0") + (version "1.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "0si1x2bi5pff1dicpqg7hv4ziq46vm7lic72724ljsclpz9bfv6q")))) + "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs @@ -3103,13 +3147,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.30.2") + (version "1.30.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0rqvwhs6d8ls1rq7j5ywl5k0qgblxpzimilyw335bi1yad5s10h3")))) + "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -3142,7 +3186,7 @@ powerful online queries from gene annotation to database mining.") (string-append m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) (propagated-inputs - (list r-futile-logger r-snow r-bh)) + (list r-bh r-codetools r-futile-logger r-snow)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocParallel") @@ -3934,13 +3978,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.48.1") + (version "1.48.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "18ain5s0ry6w0ki4c0czvwax2ncigrldyac30a6mlbzyaga6i54h")))) + "0f14p1ma2y8l60p9sxmh5j0axws9by1cznczb2jxipphpb4slpl1")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -4193,14 +4237,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.36.0") + (version "1.36.2") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0hzlm6nzmx0iyjh063512a3ghc1xqb58g5z2bnd2wl4y42iww7bg")))) + "1rn03w8y80prbvzahkvf8275haiymnjj1ijcgn55p3d0sb54yzgw")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -4932,14 +4976,14 @@ tab-delimited (tabix) files.") (define-public r-restfulr (package (name "r-restfulr") - (version "0.0.13") + (version "0.0.14") (source (origin (method url-fetch) (uri (cran-uri "restfulr" version)) (sha256 (base32 - "1dk45mzrr6ka92yjz7hfhkj12kpx1wg4szv1h1mg80mgga4ganbv")))) + "1sdlz8zl4xvd7cpn1gm86q7jv9v7561gg4wk6y7zybiw37pxghq6")))) (properties `((upstream-name . "restfulr"))) (build-system r-build-system) (propagated-inputs @@ -5909,13 +5953,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.6.1") + (version "1.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "1w3qi35vk289cpky1pb0wgg1hr55s5kdw7np98i9c1vmwi3gvwr7")))) + (base32 "0s1n3impm4k55pac8mr18czylsc30yqcvdfdki4sawk74b2rkx8c")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs @@ -6383,14 +6427,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.30.0") + (version "3.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1ch636j3zd6hcfnl455vjs36wffrdhwzyvkbikcwjg7idiknjdkf")))) + "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -7368,14 +7412,14 @@ and summarizing a set of statistics using a weighted distance approach.") (define-public r-nbpseq (package (name "r-nbpseq") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "NBPSeq" version)) (sha256 (base32 - "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) + "07mnnk4n0cyksp1mw36y6369is62kxsfg3wb8d3dwswycdmj8m14")))) (properties `((upstream-name . "NBPSeq"))) (build-system r-build-system) (propagated-inputs @@ -7652,14 +7696,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.24.0") + (version "2.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "1fyqd7qhij2iyx9vdmgnx2qf0w3kwbkmg805539zrmxry8cwfldb")))) + "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -8699,14 +8743,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.4.1") + (version "4.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "03bg3agisrm4q10gg57dksvd1ws37if6a1gwcxaybb4c50zadm8p")))) + "07fbc3d06990qy1qcaqqgm5ma2l0h08bwfkqrnlfd9f2xcppdywd")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -10768,14 +10812,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.10.1") + (version "2.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "1cf80gmzz4c1pvif3350ifsmsbfplyl2na39n8g3x0zkwpl6ijdc")))) + "1pvyx8nxv10s816hgxrnw60hp9rlqjdgjq3ajpzqxgxmmlhnk0v0")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -12235,14 +12279,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "0n2msyyy1xhapkd66j4xwabg4qfd62l01p1nmafjwifnjsx45xvp")))) + "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -13806,14 +13850,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "0s9vj74359ckmwl8r951jxrzkidslwdl9qamkhz8ilw8b5awxyw4")))) + "1r1lg7k60qgb489xkypd4gvm1fmdlihvylb5va6xj58ipndbfday")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs |