[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
01/13: gnu: r-fourcseq: Move to (gnu packages bioconductor).
From: |
guix-commits |
Subject: |
01/13: gnu: r-fourcseq: Move to (gnu packages bioconductor). |
Date: |
Mon, 14 Sep 2020 15:39:48 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit f4d920b9f7ac404b245693fe21b39b7c41a49a61
Author: zimoun <zimon.toutoune@gmail.com>
AuthorDate: Mon Sep 14 18:07:36 2020 +0200
gnu: r-fourcseq: Move to (gnu packages bioconductor).
* gnu/packages/cran.scm (r-fourcseq): Move from here...
* gnu/packages/bioconductor.scm (r-fourcseq): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++++
gnu/packages/cran.scm | 44 ------------------------------------------
2 files changed, 45 insertions(+), 44 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a9f8ff2..5505747 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4,6 +4,7 @@
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
+;;; Copyright © 2020 Mădălin Ionel Patrașcu
<madalinionel.patrascu@mdc-berlin.de>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -8242,3 +8243,47 @@ with:
@end itemize
")
(license license:gpl2+)))
+
+(define-public r-fourcseq
+ (package
+ (name "r-fourcseq")
+ (version "1.22.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "FourCSeq" version))
+ (sha256
+ (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
+ (properties `((upstream-name . "FourCSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biostrings" ,r-biostrings)
+ ("r-deseq2" ,r-deseq2)
+ ("r-fda" ,r-fda)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggbio" ,r-ggbio)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gtools" ,r-gtools)
+ ("r-lsd" ,r-lsd)
+ ("r-matrix" ,r-matrix)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page
+ "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
+ (synopsis "Analysis of multiplexed 4C sequencing data")
+ (description
+ "This package is an R package dedicated to the analysis of (multiplexed)
+4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
+interactions between DNA elements and identify differential interactions
+between conditions. The statistical analysis in R starts with individual bam
+files for each sample as inputs. To obtain these files, the package contains
+a Python script to demultiplex libraries and trim off primer sequences. With
+a standard alignment software the required bam files can be then be
+generated.")
+ (license license:gpl3+)))
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a39c0e6..5169800 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22575,50 +22575,6 @@ Try a demo of the LSD by running @code{demotour()}.")
;; Either version
(license (list license:gpl2 license:gpl3))))
-(define-public r-fourcseq
- (package
- (name "r-fourcseq")
- (version "1.22.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "FourCSeq" version))
- (sha256
- (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
- (properties `((upstream-name . "FourCSeq")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biostrings" ,r-biostrings)
- ("r-deseq2" ,r-deseq2)
- ("r-fda" ,r-fda)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggbio" ,r-ggbio)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gtools" ,r-gtools)
- ("r-lsd" ,r-lsd)
- ("r-matrix" ,r-matrix)
- ("r-reshape2" ,r-reshape2)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page
- "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
- (synopsis "Analysis of multiplexed 4C sequencing data")
- (description
- "This package is an R package dedicated to the analysis of (multiplexed)
-4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
-interactions between DNA elements and identify differential interactions
-between conditions. The statistical analysis in R starts with individual bam
-files for each sample as inputs. To obtain these files, the package contains
-a Python script to demultiplex libraries and trim off primer sequences. With
-a standard alignment software the required bam files can be then be
-generated.")
- (license license:gpl3+)))
-
(define-public r-phylogram
(package
(name "r-phylogram")
- branch master updated (62881be -> 3159fcf), guix-commits, 2020/09/14
- 01/13: gnu: r-fourcseq: Move to (gnu packages bioconductor).,
guix-commits <=
- 02/13: gnu: r-preprocesscore: Move to (gnu packages bioconductor)., guix-commits, 2020/09/14
- 03/13: gnu: r-rgraphviz: Move to (gnu packages bioconductor)., guix-commits, 2020/09/14
- 04/13: gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor)., guix-commits, 2020/09/14
- 05/13: gnu: r-scran: Move to (gnu packages bioconductor)., guix-commits, 2020/09/14
- 06/13: gnu: r-scater: Move to (gnu packages bioconductor)., guix-commits, 2020/09/14
- 09/13: gnu: r-rhdf5lib: Move to (gnu packages bioconductor)., guix-commits, 2020/09/14
- 07/13: gnu: r-singlecellexperiment: Move to (gnu packages bioconductor)., guix-commits, 2020/09/14
- 08/13: gnu: r-beachmat: Move to (gnu packages bioconductor)., guix-commits, 2020/09/14
- 11/13: gnu: r-hitc: Move to (gnu packages bioconductor)., guix-commits, 2020/09/14
- 12/13: gnu: r-fithic: Move to (gnu packages bioconductor)., guix-commits, 2020/09/14