unofficial mirror of guix-patches@gnu.org 
 help / color / mirror / code / Atom feed
* [bug#56024] [PATCH] gnu: Add r-alpine.
@ 2022-06-16 17:00 Mădălin Ionel Patrașcu
  2022-11-24 13:44 ` bug#56024: " Ricardo Wurmus
  0 siblings, 1 reply; 2+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-06-16 17:00 UTC (permalink / raw)
  To: 56024

* gnu/packages/bioconductor.scm (r-alpine): New variable.
---
 gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1e87b190c2..e0797206f1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1987,6 +1987,46 @@ (define-public r-agimicrorna
 objects are used so that other packages could be used as well.")
     (license license:gpl3)))
 
+(define-public r-alpine
+  (package
+    (name "r-alpine")
+    (version "1.22.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "alpine" version))
+              (sha256
+               (base32
+                "1nl1hxwakh5m9rqm3ksn2jzknsj9xnwl51bmc30knknm4q35wdv9"))))
+    (properties `((upstream-name . "alpine")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-graph
+           r-iranges
+           r-rbgl
+           r-rsamtools
+           r-s4vectors
+           r-speedglm
+           r-stringr
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/alpine")
+    (synopsis "Modeling and correcting fragment sequence bias")
+    (description
+     "The package @code{alpine} helps to model bias parameters and then using
+those parameters to estimate RNA-seq transcript abundance.  @code{Alpine} is a
+package for estimating and visualizing many forms of sample-specific biases that
+can arise in RNA-seq, including fragment length distribution, positional bias on
+the transcript, read start bias (random hexamer priming), and fragment GC-content
+(amplification).  It also offers bias-corrected estimates of transcript abundance
+in @dfn{FPKM}(Fragments Per Kilobase of transcript per Million mapped reads).  It
+is currently designed for un-stranded paired-end RNA-seq data.")
+    (license license:gpl2+)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")

base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb
-- 
2.36.1





^ permalink raw reply related	[flat|nested] 2+ messages in thread

* bug#56024: [PATCH] gnu: Add r-alpine.
  2022-06-16 17:00 [bug#56024] [PATCH] gnu: Add r-alpine Mădălin Ionel Patrașcu
@ 2022-11-24 13:44 ` Ricardo Wurmus
  0 siblings, 0 replies; 2+ messages in thread
From: Ricardo Wurmus @ 2022-11-24 13:44 UTC (permalink / raw)
  To: 56024-done

Applied, thanks!

-- 
Ricardo




^ permalink raw reply	[flat|nested] 2+ messages in thread

end of thread, other threads:[~2022-11-24 13:45 UTC | newest]

Thread overview: 2+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2022-06-16 17:00 [bug#56024] [PATCH] gnu: Add r-alpine Mădălin Ionel Patrașcu
2022-11-24 13:44 ` bug#56024: " Ricardo Wurmus

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).