GNU bug report logs - #61921
[PATCH] gnu: Add r-oscope.

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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>
Cc: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-oscope.
Date: Thu, 2 Mar 2023 16:48:03 +0000

* gnu/packages/bioconductor.scm (r-oscope): New variable.
---
 gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2bfca85bbc..c4fb44f7b2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1702,6 +1702,37 @@ (define-public r-curatedtcgadata
 across the entire multi-'omics experiment.")
     (license license:artistic2.0)))
 
+(define-public r-oscope
+  (let ((commit "32e0ea72236128731f35a60fb5abcde5b5d35433")
+        (revision "1"))
+    (package
+      (name "r-oscope")
+      (version (git-version "1.29.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.bioconductor.org/packages/Oscope")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "02929i7zd4fwdhxi0h2i7y3sn6v1k3srahn5a6v9wvihp5nmgcig"))))
+      (properties `((upstream-name . "Oscope")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat))
+      (home-page "https://git.bioconductor.org/packages/Oscope")
+      (synopsis
+       "Oscillatory 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-parathyroidse
   (package
     (name "r-parathyroidse")
-- 
2.34.1

Message #10 received at 61921-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 61921-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-oscope.
Date: Fri, 03 Mar 2023 12:57:14 +0100

Superseded by issue 61931.

-- 
Ricardo

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