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05/10: gnu: Add r-atena.
From: |
guix-commits |
Subject: |
05/10: gnu: Add r-atena. |
Date: |
Thu, 27 Oct 2022 10:40:53 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit c0278aa51e08bc5c9916f2b58b7b45676863844f
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Thu Jun 23 12:25:20 2022 +0200
gnu: Add r-atena.
* gnu/packages/bioconductor.scm (r-atena): New variable.
---
gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6e72a8e1af..038532c915 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2317,6 +2317,47 @@ reproducible gene expression signatures capable of
accurately distinguishing
tumor samples from healthy controls.")
(license license:artistic2.0)))
+(define-public r-atena
+ (package
+ (name "r-atena")
+ (version "1.2.2")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "atena" version))
+ (sha256
+ (base32
+ "0b89wb7cc44c8jd6868dn8pwgid768bprkncsi87qkdz0abbhzhp"))))
+ (properties `((upstream-name . "atena")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-annotationhub
+ r-biocgenerics
+ r-biocparallel
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-iranges
+ r-matrix
+ r-rsamtools
+ r-s4vectors
+ r-scales
+ r-sparsematrixstats
+ r-squarem
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/functionalgenomics/atena")
+ (synopsis "Analysis of transposable elements")
+ (description
+ "The atena package quantifies expression of @dfn{TEs} (transposable
+elements) from RNA-seq data through different methods, including ERVmap,
+TEtranscripts and Telescope. A common interface is provided to use each of
+these methods, which consists of building a parameter object, calling the
+quantification function with this object and getting a
+@code{SummarizedExperiment} object as an output container of the quantified
+expression profiles. The implementation allows quantifing TEs and gene
+transcripts in an integrated manner.")
+ (license license:artistic2.0)))
+
(define-public r-atsnp
(package
(name "r-atsnp")
- branch master updated (d9686315bd -> aef2425666), guix-commits, 2022/10/27
- 05/10: gnu: Add r-atena.,
guix-commits <=
- 04/10: gnu: Add r-atsnp., guix-commits, 2022/10/27
- 09/10: gnu: Add r-asgsca., guix-commits, 2022/10/27
- 03/10: gnu: Add r-attract., guix-commits, 2022/10/27
- 07/10: gnu: Add r-assessorf., guix-commits, 2022/10/27
- 10/10: gnu: Add r-aseb., guix-commits, 2022/10/27
- 08/10: gnu: Add r-aspli., guix-commits, 2022/10/27
- 06/10: gnu: Add r-asset., guix-commits, 2022/10/27
- 01/10: gnu: Add r-awst., guix-commits, 2022/10/27
- 02/10: gnu: Add r-awfisher., guix-commits, 2022/10/27