From: Navid Afkhami <navid.afkhami@mdc-berlin.de>
To: 61921@debbugs.gnu.org
Cc: Navid Afkhami <navid.afkhami@mdc-berlin.de>
Subject: [bug#61921] [PATCH] gnu: Add r-oscope.
Date: Thu, 2 Mar 2023 16:48:03 +0000 [thread overview]
Message-ID: <20230302164803.71966-1-navid.afkhami@mdc-berlin.de> (raw)
* 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
next reply other threads:[~2023-03-02 16:49 UTC|newest]
Thread overview: 2+ messages / expand[flat|nested] mbox.gz Atom feed top
2023-03-02 16:48 Navid Afkhami [this message]
2023-03-03 11:57 ` bug#61921: [PATCH] gnu: Add r-oscope Ricardo Wurmus
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