GNU bug report logs - #61931
[PATCH] gnu: Add r-oscope.

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 61931 in the body.
You can then email your comments to 61931 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-oscope.
Date: Fri, 3 Mar 2023 11:56:25 +0100

* gnu/packages/bioconductor.scm (r-oscope): New variable.
---
 gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 22be8d3772..78eb24625f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7425,6 +7425,32 @@ (define-public r-organismdbi
 the fact that each of these packages implements a select methods.")
     (license license:artistic2.0)))
 
+(define-public r-oscope
+  (package
+    (name "r-oscope")
+    (version "1.28.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Oscope" version))
+              (sha256
+               (base32
+                "0454f9yc0jmg3mcq9264wb5v2n8n0kaf801hlvsiy1xa3baj3h29"))))
+    (properties `((upstream-name . "Oscope")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat))
+    (home-page "https://bioconductor.org/packages/Oscope")
+    (synopsis
+     "Scillatory genes identifier in unsynchronized single cell RNA-seq")
+    (description
+     "Oscope is a oscillatory genes identifier in unsynchronized single cell RNA-seq.
+This statistical pipeline has been developed to identify and recover the
+base cycle profiles of oscillating genes in an unsynchronized single cell
+RNA-seq experiment.  The Oscope pipeline includes three modules: a sine model
+module to search for candidate oscillator pairs; a K-medoids clustering module
+to cluster candidate oscillators into groups; and an extended nearest insertion
+module to recover the base cycle order for each oscillator group.")
+    (license license:asl2.0)))
+
 (define-public r-pcaexplorer
   (package
     (name "r-pcaexplorer")
-- 
2.34.1

Message #10 received at 61931-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 61931-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-oscope.
Date: Fri, 03 Mar 2023 12:05:25 +0100

Thanks for the patch.  I have applied it with commit
4f681cdbc27e6a922f24d4297efe3c0b823195f0.

-- 
Ricardo

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.