From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <56819@debbugs.gnu.org>
Cc: rekado@elephly.net
Subject: [bug#56819] [PATCH 2/2] gnu: Add r-infercnv.
Date: Thu, 28 Jul 2022 23:38:59 +0200 [thread overview]
Message-ID: <20220728213859.21641-2-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <20220728213859.21641-1-madalinionel.patrascu@mdc-berlin.de>
* gnu/packages/bioconductor.scm (r-infercnv): New variable.
---
gnu/packages/bioconductor.scm | 60 +++++++++++++++++++++++++++++++++++
1 file changed, 60 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 31484799b2..e9bfbed9b5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -49,6 +49,7 @@ (define-module (gnu packages bioconductor)
#:use-module (gnu packages image)
#:use-module (gnu packages maths)
#:use-module (gnu packages netpbm)
+ #:use-module (gnu packages python)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages statistics)
@@ -2647,6 +2648,65 @@ (define-public r-ideoviz
arbitrary genomic intervals along chromosomal ideogram.")
(license license:gpl2)))
+(define-public r-infercnv
+ (package
+ (name "r-infercnv")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "infercnv" version))
+ (sha256
+ (base32
+ "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
+ (properties `((upstream-name . "infercnv")))
+ (build-system r-build-system)
+ (inputs (list python))
+ (propagated-inputs
+ (list r-ape
+ r-argparse
+ r-biocgenerics
+ r-catools
+ r-coda
+ r-coin
+ r-digest
+ r-doparallel
+ r-dplyr
+ r-edger
+ r-fastcluster
+ r-fitdistrplus
+ r-foreach
+ r-futile-logger
+ r-future
+ r-ggplot2
+ r-gplots
+ r-gridextra
+ r-hiddenmarkov
+ r-leiden
+ r-matrix
+ r-paralleldist
+ r-phyclust
+ r-rann
+ r-rcolorbrewer
+ r-reshape
+ r-rjags
+ r-singlecellexperiment
+ r-summarizedexperiment
+ r-tidyr))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/broadinstitute/inferCNV/wiki")
+ (synopsis "Infer copy number variation from single-cell RNA-Seq data")
+ (description
+ "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify
+evidence for somatic large-scale chromosomal copy number alterations, such as gains
+or deletions of entire chromosomes or large segments of chromosomes. This is done
+by exploring expression intensity of genes across positions of a tumor genome in
+comparison to a set of reference \"normal\" cells. A heatmap is generated
+illustrating the relative expression intensities across each chromosome, and it
+often becomes readily apparent as to which regions of the tumor genome are
+over-abundant or less-abundant as compared to that of normal cells.")
+ (license license:bsd-3)))
+
(define-public r-iranges
(package
(name "r-iranges")
--
2.37.1
next prev parent reply other threads:[~2022-07-28 21:40 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-07-28 21:35 [bug#56819] gnu: Add r-phyclust and r-infercnv. (New variables) MadalinIonel.Patrascu
2022-07-28 21:38 ` [bug#56819] [PATCH 1/2] gnu: Add r-phyclust Mădălin Ionel Patrașcu
2022-07-28 21:38 ` Mădălin Ionel Patrașcu [this message]
2022-08-01 14:20 ` [bug#56819] [PATCH 2/2] gnu: Add r-infercnv Ricardo Wurmus
2022-08-02 8:23 ` bug#56819: " Ricardo Wurmus
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://guix.gnu.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=20220728213859.21641-2-madalinionel.patrascu@mdc-berlin.de \
--to=madalinionel.patrascu@mdc-berlin.de \
--cc=56819@debbugs.gnu.org \
--cc=rekado@elephly.net \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).