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branch master updated: gnu: Add r-tradeseq.
From: |
guix-commits |
Subject: |
branch master updated: gnu: Add r-tradeseq. |
Date: |
Thu, 27 May 2021 07:40:42 -0400 |
This is an automated email from the git hooks/post-receive script.
roelj pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new cf9ddbd gnu: Add r-tradeseq.
cf9ddbd is described below
commit cf9ddbd4bcd0f5c76234e03d7986f8639d11bd83
Author: Roel Janssen <roel@gnu.org>
AuthorDate: Thu May 27 13:40:10 2021 +0200
gnu: Add r-tradeseq.
* gnu/packages/bioconductor.scm (r-tradeseq): New variable.
---
gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8ca0521..b58c5bc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5013,6 +5013,51 @@ Fisher, Stouffer, Tippett, and Wilkinson; a number of
data-sets to replicate
published results; and a routine for graphical display.")
(license license:gpl2)))
+(define-public r-tradeseq
+ (package
+ (name "r-tradeseq")
+ (version "1.4.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "tradeSeq" version))
+ (sha256
+ (base32
+ "1ncmvn9kaksismvsjs042xsp8bfq1xnm0ds87dwpk95bnpj96a89"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-clusterexperiment" ,r-clusterexperiment)
+ ("r-dplyr" ,r-dplyr)
+ ("r-edger" ,r-edger)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-igraph" ,r-igraph)
+ ("r-magrittr" ,r-magrittr)
+ ("r-mgcv" ,r-mgcv)
+ ("r-monocle" ,r-monocle)
+ ("r-pbapply" ,r-pbapply)
+ ("r-princurve" ,r-princurve)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-slingshot" ,r-slingshot)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-tibble" ,r-tibble)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://statomics.github.io/tradeSeq/index.html")
+ (synopsis "Trajectory-based differential expression analysis")
+ (description
+ "This package provides a flexible method for fitting regression models that
+can be used to find genes that are differentially expressed along one or
+multiple lineages in a trajectory. Based on the fitted models, it uses a
+variety of tests suited to answer different questions of interest, e.g. the
+discovery of genes for which expression is associated with pseudotime, or which
+are differentially expressed (in a specific region) along the trajectory. It
+fits a negative binomial generalized additive model (GAM) for each gene, and
+performs inference on the parameters of the GAM.")
+ (license license:expat)))
+
(define-public r-triform
(package
(name "r-triform")
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