diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 77 |
1 files changed, 53 insertions, 24 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a8ed2707ac..b191c8b4ae 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1396,14 +1396,14 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "10i21gxv0n7lrflhj5ja672xjizy1i4y4iq3pmjgbf0dpy1lxsih")))) + "0bzjwzj5mvb49wgvs3gd3jfpm7s0zfkca763i65i7m994lgvz33c")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -1587,7 +1587,7 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") ("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "http://github.com/jdstorey/qvalue") + (home-page "https://github.com/StoreyLab/qvalue") (synopsis "Q-value estimation for false discovery rate control") (description "This package takes a list of p-values resulting from the simultaneous @@ -2934,7 +2934,7 @@ qPCR data, but could be used with other types as well.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/cole-trapnell-lab/monocle3.git") + (url "https://github.com/cole-trapnell-lab/monocle3") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -5119,14 +5119,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "15l8f7ls2mwhsw68sr1k4r19hmdzjriibr5hpnfbanzj5x6yhdjq")))) + "1wknigh1md3w4h68caqlpq945maipdkpmw10hc2rlx4nbbpcnawp")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -5781,14 +5781,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.2.2") + (version "2.2.4") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "1wgilpaw70dwg0zilx5i1pmi4j8wri6wi2ha1d3bapfhlwc6igml")))) + "0yznfqgp5cbz68n3rrfvm752267da16kl538zdrb1g1aw9zdfqc6")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -6248,14 +6248,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.0.0") + (version "2.0.5") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "0zpq2j4y9i5lls1kj2w4spl8qjp3076idsr2a2rjvy1fykzlp01q")))) + "174brv027mm90lydfg6hnhazwh8jy4vf6ial4hpsfalwa5jrz55n")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs @@ -6286,6 +6286,7 @@ sequential way to mimic the manual gating strategy.") ("r-runit" ,r-runit) ("r-tibble" ,r-tibble) ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2) ("r-yaml" ,r-yaml))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -6373,14 +6374,14 @@ delete entire rows with missing data.") (define-public r-depecher (package (name "r-depecher") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "0nmx04qybzf6nhfngmdxwpbbz9x32v34mbnpg8jq7a2cgchzsj9s")))) + "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs @@ -6455,14 +6456,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0n78lf5hz6zzl550dbf4imis43pv91zicfff8y4lspckljhz9z75")))) + "0nf9yqg5krj26n4n82iyx3rsr84d46b17i9zfk35sh12l4xssbii")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -6482,6 +6483,7 @@ genes in the gene-set that are ranked above the leading edge).") ("r-plyr" ,r-plyr) ("r-reshape2" ,r-reshape2) ("r-s4vectors" ,r-s4vectors) + ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) @@ -6507,7 +6509,7 @@ accessibility data.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/cole-trapnell-lab/cicero-release.git") + (url "https://github.com/cole-trapnell-lab/cicero-release") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -6528,7 +6530,7 @@ accessibility data.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/aertslab/cisTopic.git") + (url "https://github.com/aertslab/cisTopic") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -6673,14 +6675,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "00hggma0i15w03xi9jr02v2593jbqkcxyfcvpp7mdzrshn99m9p6")) + "0ipf60wylbhvwk9q3mbnak0f1n6k7spfh90s1c1c0b47ryxsri67")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -7046,14 +7048,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.18.0") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "1rn655qq7dshbk1dd41n7y2hfz8498jxd2j4rk7p8hrikd3s32dm")))) + "19bhkb8vd44m3nkznw075fx3y2p3a1bsazbhcfiqw9n4190k9bgv")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -7185,21 +7187,20 @@ using whole genome sequencing data.") (define-public r-activepathways (package (name "r-activepathways") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "ActivePathways" version)) (sha256 (base32 - "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20")))) + "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l")))) (properties `((upstream-name . "ActivePathways"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2) - ("r-metap" ,r-metap))) + ("r-ggplot2" ,r-ggplot2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/ActivePathways/") @@ -8087,3 +8088,31 @@ metrics, such as the elbow method and Horn's parallel analysis, which has relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high dimensional mass cytometry data.") (license license:gpl3))) + +(define-public r-rgreat + (package + (name "r-rgreat") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rGREAT" version)) + (sha256 + (base32 + "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v")))) + (properties `((upstream-name . "rGREAT"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicranges" ,r-genomicranges) + ("r-getoptlong" ,r-getoptlong) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rjson" ,r-rjson))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jokergoo/rGREAT") + (synopsis "Client for GREAT analysis") + (description + "This package makes GREAT (Genomic Regions Enrichment of Annotations +Tool) analysis automatic by constructing a HTTP POST request according to +user's input and automatically retrieving results from GREAT web server.") + (license license:expat))) |