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bug#61931: closed ([PATCH] gnu: Add r-oscope.)

From: GNU bug Tracking System
Subject: bug#61931: closed ([PATCH] gnu: Add r-oscope.)
Date: Fri, 03 Mar 2023 11:07:02 +0000

Your message dated Fri, 03 Mar 2023 12:05:25 +0100
with message-id <87pm9qdrh8.fsf@elephly.net>
and subject line [PATCH] gnu: Add r-oscope.
has caused the debbugs.gnu.org bug report #61931,
regarding [PATCH] gnu: Add r-oscope.
to be marked as done.

(If you believe you have received this mail in error, please contact

61931: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=61931
GNU Bug Tracking System
Contact help-debbugs@gnu.org with problems
--- Begin Message --- 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 
+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
     (name "r-pcaexplorer")

--- End Message ---
--- Begin Message --- Subject: [PATCH] gnu: Add r-oscope. Date: Fri, 03 Mar 2023 12:05:25 +0100 User-agent: mu4e 1.8.13; emacs 28.2
Thanks for the patch.  I have applied it with commit


--- End Message ---

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