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269/323: gnu: Add r-msmstests.
From: |
guix-commits |
Subject: |
269/323: gnu: Add r-msmstests. |
Date: |
Mon, 7 Dec 2020 15:14:12 -0500 (EST) |
rekado pushed a commit to branch wip-r
in repository guix.
commit 793ee5fa704a3d58de69276170aef9abc81405ee
Author: zimoun <zimon.toutoune@gmail.com>
AuthorDate: Fri Dec 4 02:08:41 2020 +0100
gnu: Add r-msmstests.
* gnu/packages/bioconductor.scm (r-msmstests): New variable.
---
gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++
1 file changed, 32 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index cfb59fc..3ad28e1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9016,3 +9016,35 @@ as well as local access. Developers can register a file
extension, e.g.,
"Exploratory data analysis to assess the quality of a set of LC-MS/MS
experiments, and visualize de influence of the involved factors.")
(license license:gpl2)))
+
+(define-public r-msmstests
+ (package
+ (name "r-msmstests")
+ (version "1.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "msmsTests" version))
+ (sha256
+ (base32
+ "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
+ (properties `((upstream-name . "msmsTests")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-edger" ,r-edger)
+ ("r-msmseda" ,r-msmseda)
+ ("r-msnbase" ,r-msnbase)
+ ("r-qvalue" ,r-qvalue)))
+ (home-page
+ "https://bioconductor.org/packages/msmsTests")
+ (synopsis "Differential LC-MS/MS expression tests")
+ (description
+ "This packages provides statistical tests for label-free LC-MS/MS data
+by spectral counts, to discover differentially expressed proteins between two
+biological conditions. Three tests are available: Poisson GLM regression,
+quasi-likelihood GLM regression, and the negative binomial of the edgeR
+package.The three models admit blocking factors to control for nuissance
+variables.To assure a good level of reproducibility a post-test filter is
+available, where we may set the minimum effect size considered biologicaly
+relevant, and the minimum expression of the most abundant condition.")
+ (license license:gpl2)))
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- 170/323: gnu: r-hyperdraw: Update to 1.42.0., guix-commits, 2020/12/07
- 178/323: gnu: r-reactomepa: Update to 1.34.0., guix-commits, 2020/12/07
- 177/323: gnu: r-graphite: Update to 1.36.0., guix-commits, 2020/12/07
- 199/323: gnu: r-hitc: Update to 1.34.0., guix-commits, 2020/12/07
- 204/323: gnu: r-delayedarray: Update to 0.16.0., guix-commits, 2020/12/07
- 52/323: gnu: r-ebseq: Update to 1.30.0., guix-commits, 2020/12/07
- 237/323: gnu: r-rsamtools: Update to 2.6.0., guix-commits, 2020/12/07
- 244/323: gnu: r-bsgenome: Update to 1.58.0., guix-commits, 2020/12/07
- 249/323: gnu: r-zlibbioc: Update to 1.36.0., guix-commits, 2020/12/07
- 269/323: gnu: Add r-msmstests.,
guix-commits <=
- 251/323: gnu: r-bamsignals: Update to 1.22.0., guix-commits, 2020/12/07
- 253/323: gnu: r-mutationalpatterns: Update to 3.0.1., guix-commits, 2020/12/07
- 261/323: gnu: r-mzr: Update to 2.24.1., guix-commits, 2020/12/07
- 278/323: gnu: r-genomicfiles: Update to 1.26.0., guix-commits, 2020/12/07
- 282/323: gnu: r-organismdbi: Update to 1.32.0., guix-commits, 2020/12/07
- 277/323: gnu: r-gage: Update to 2.40.0., guix-commits, 2020/12/07
- 130/323: gnu: r-annotatr: Update to 1.16.0., guix-commits, 2020/12/07
- 233/323: gnu: r-annotationdbi: Update to 1.52.0., guix-commits, 2020/12/07
- 235/323: gnu: r-biocparallel: Update to 1.24.1., guix-commits, 2020/12/07
- 238/323: gnu: r-summarizedexperiment: Update to 1.20.0., guix-commits, 2020/12/07