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branch master updated: gnu: Add r-transcriptr.
From: |
guix-commits |
Subject: |
branch master updated: gnu: Add r-transcriptr. |
Date: |
Tue, 11 Jan 2022 08:50:00 -0500 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new 61a1c3f72d gnu: Add r-transcriptr.
61a1c3f72d is described below
commit 61a1c3f72df3b0333865d6071beaea60294f2ce7
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Tue Jan 11 14:47:36 2022 +0100
gnu: Add r-transcriptr.
* gnu/packages/bioconductor.scm (r-transcriptr): New variable.
---
gnu/packages/bioconductor.scm | 50 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6eb34c3793..0fbe0965c2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4472,6 +4472,56 @@ this package. It also provides functionalities for
visualizing, summarizing
and comparing the clusterings.")
(license license:expat)))
+(define-public r-transcriptr
+ (package
+ (name "r-transcriptr")
+ (version "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "transcriptR" version))
+ (sha256
+ (base32 "1p5l2z3szx3qh02x7r81ajl7yc5wqsri6q6pzw83livmalcli5yy"))))
+ (properties `((upstream-name . "transcriptR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocgenerics
+ r-caret
+ r-chipseq
+ r-e1071
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-proc
+ r-reshape2
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/transcriptR")
+ (synopsis "Primary transcripts detection and quantification")
+ (description
+ "The differences in the RNA types being sequenced have an impact on the
+resulting sequencing profiles. mRNA-seq data is enriched with reads derived
+from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial
+broader coverage of both exonic and intronic regions. The presence of
+intronic reads in GRO-seq type of data makes it possible to use it to
+computationally identify and quantify all de novo continuous regions of
+transcription distributed across the genome. This type of data, however, is
+more challenging to interpret and less common practice compared to mRNA-seq.
+One of the challenges for primary transcript detection concerns the
+simultaneous transcription of closely spaced genes, which needs to be properly
+divided into individually transcribed units. The R package transcriptR
+combines RNA-seq data with ChIP-seq data of histone modifications that mark
+active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to
+overcome this challenge. The advantage of this approach over the use of, for
+example, gene annotations is that this approach is data driven and therefore
+able to deal also with novel and case specific events.")
+ (license license:gpl3)))
+
(define-public r-trajectoryutils
(package
(name "r-trajectoryutils")
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