From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: 58522@debbugs.gnu.org
Subject: [bug#58522] [PATCH] gnu: Add r-fishpond. X-Debbugs-Cc: rekado@elephly.net
Date: Fri, 14 Oct 2022 19:01:42 +0200 [thread overview]
Message-ID: <20221014170142.3204-1-madalinionel.patrascu@mdc-berlin.de> (raw)
* gnu/packages/bioconductor.scm (r-fishpond): New variable.
---
gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ecb60f2e24..c23520175d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14522,6 +14522,44 @@ (define-public r-rgraphviz
objects from the @code{graph} package.")
(license license:epl1.0)))
+(define-public r-fishpond
+ (package
+ (name "r-fishpond")
+ (version "2.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "fishpond" version))
+ (sha256
+ (base32
+ "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym"))))
+ (properties `((upstream-name . "fishpond")))
+ (build-system r-build-system)
+ (inputs (list zlib))
+ (propagated-inputs
+ (list r-abind
+ r-genomicranges
+ r-gtools
+ r-iranges
+ r-jsonlite
+ r-matrix
+ r-matrixstats
+ r-qvalue
+ r-rcpp
+ r-s4vectors
+ r-singlecellexperiment
+ r-summarizedexperiment
+ r-svmisc))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/mikelove/fishpond")
+ (synopsis "Downstream methods and tools for expression data")
+ (description
+ "The @code{fishpond} package contains methods for differential transcript
+and gene expression analysis of RNA-seq data using inferential replicates for
+uncertainty of abundance quantification, as generated by Gibbs sampling or
+bootstrap sampling. Also the package contains a number of utilities for working
+with @code{Salmon} and @code{Alevin} quantification files.")
+ (license license:gpl2)))
+
(define-public r-fithic
(package
(name "r-fithic")
base-commit: 10d429f2fce321d8285684503094694ec3979865
--
2.37.3
next reply other threads:[~2022-10-14 17:03 UTC|newest]
Thread overview: 2+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-10-14 17:01 Mădălin Ionel Patrașcu [this message]
2022-10-27 13:24 ` bug#58522: [PATCH] gnu: Add r-fishpond 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=20221014170142.3204-1-madalinionel.patrascu@mdc-berlin.de \
--to=madalinionel.patrascu@mdc-berlin.de \
--cc=58522@debbugs.gnu.org \
/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).