* [bug#50570] [PATCH 0/2] R packages @ 2021-09-13 14:18 zimoun 2021-09-13 14:20 ` [bug#50570] [PATCH 1/2] gnu: Add r-simplifyenrichment zimoun 2021-09-20 20:13 ` bug#50570: [PATCH 0/2] R packages Ricardo Wurmus 0 siblings, 2 replies; 4+ messages in thread From: zimoun @ 2021-09-13 14:18 UTC (permalink / raw) To: 50570; +Cc: zimoun, rekado Hi, Trivial addition. The package r-presto does not have a tag version, hence the commit; they say in README about CRAN but the archive does not contain it, or I miss it. All the best, simon zimoun (2): gnu: Add r-simplifyenrichment. gnu: Add r-presto. gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++ 2 files changed, 74 insertions(+) base-commit: 53f54d4aa252fed425180641f27094600522c4f1 -- 2.32.0 ^ permalink raw reply [flat|nested] 4+ messages in thread
* [bug#50570] [PATCH 1/2] gnu: Add r-simplifyenrichment. 2021-09-13 14:18 [bug#50570] [PATCH 0/2] R packages zimoun @ 2021-09-13 14:20 ` zimoun 2021-09-13 14:20 ` [bug#50570] [PATCH 2/2] gnu: Add r-presto zimoun 2021-09-20 20:13 ` bug#50570: [PATCH 0/2] R packages Ricardo Wurmus 1 sibling, 1 reply; 4+ messages in thread From: zimoun @ 2021-09-13 14:20 UTC (permalink / raw) To: 50570; +Cc: zimoun * gnu/packages/bioconductor.scm (r-simplifyenrichment): New variable. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 25202410e5..e59ba07d23 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4236,6 +4236,46 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-simplifyenrichment + (package + (name "r-simplifyenrichment") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "simplifyEnrichment" version)) + (sha256 + (base32 + "0rqa414kvyjjmj4932zk39rqa14z13b57rkrxdrf16jmq2r437vh")))) + (properties + `((upstream-name . "simplifyEnrichment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocgenerics" ,r-biocgenerics) + ("r-circlize" ,r-circlize) + ("r-clue" ,r-clue) + ("r-cluster" ,r-cluster) + ("r-complexheatmap" ,r-complexheatmap) + ("r-digest" ,r-digest) + ("r-getoptlong" ,r-getoptlong) + ("r-go-db" ,r-go-db) + ("r-gosemsim" ,r-gosemsim) + ("r-matrix" ,r-matrix) + ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-proxyc" ,r-proxyc) + ("r-slam" ,r-slam) + ("r-tm" ,r-tm))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jokergoo/simplifyEnrichment") + (synopsis "Simplify Functional Enrichment Results") + (description "This package provides a new clustering algorithm, binary +cut, for clustering similarity matrices of functional terms is implemeted in +this package. It also provideds functionalities for visualizing, summarizing +and comparing the clusterings.") + (license license:expat))) + + (define-public r-trajectoryutils (package (name "r-trajectoryutils") -- 2.32.0 ^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#50570] [PATCH 2/2] gnu: Add r-presto. 2021-09-13 14:20 ` [bug#50570] [PATCH 1/2] gnu: Add r-simplifyenrichment zimoun @ 2021-09-13 14:20 ` zimoun 0 siblings, 0 replies; 4+ messages in thread From: zimoun @ 2021-09-13 14:20 UTC (permalink / raw) To: 50570; +Cc: zimoun * gnu/packages/bioinformatics.scm (r-presto): New variable. --- gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c3ab0ce354..647feff9ec 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki@gmail.com> ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de> +;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -7417,6 +7418,39 @@ sequence.") (supported-systems '("i686-linux" "x86_64-linux")) (license license:bsd-3))) +(define-public r-presto + (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad") + (revision "0")) + (package + (name "r-presto") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/immunogenomics/presto") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1c3fmag4r4p2lvbvxlxyck9dvfw1prbwcl9665mmlx4a35750hk8")))) + (properties `((upstream . "presto"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-deseq2" ,r-deseq2) + ("r-dplyr" ,r-dplyr) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/immunogenomics/presto") + (synopsis "Fast Functions for Differential Expression using Wilcox and AUC") + (description "This package performs a fast Wilcoxon rank sum test and +auROC analysis.") + (license license:gpl3)))) + (define-public r-snapatac (package (name "r-snapatac") -- 2.32.0 ^ permalink raw reply related [flat|nested] 4+ messages in thread
* bug#50570: [PATCH 0/2] R packages 2021-09-13 14:18 [bug#50570] [PATCH 0/2] R packages zimoun 2021-09-13 14:20 ` [bug#50570] [PATCH 1/2] gnu: Add r-simplifyenrichment zimoun @ 2021-09-20 20:13 ` Ricardo Wurmus 1 sibling, 0 replies; 4+ messages in thread From: Ricardo Wurmus @ 2021-09-20 20:13 UTC (permalink / raw) To: zimoun; +Cc: 50570-done Thank you for the patches. Pushed to the “master” branch with commit f80824fe0997f3e5d73ef16b8d42d248ce31cc69. -- Ricardo ^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2021-09-20 20:14 UTC | newest] Thread overview: 4+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2021-09-13 14:18 [bug#50570] [PATCH 0/2] R packages zimoun 2021-09-13 14:20 ` [bug#50570] [PATCH 1/2] gnu: Add r-simplifyenrichment zimoun 2021-09-13 14:20 ` [bug#50570] [PATCH 2/2] gnu: Add r-presto zimoun 2021-09-20 20:13 ` bug#50570: [PATCH 0/2] R packages Ricardo Wurmus
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