[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
02/23: gnu: Add r-hsmmsinglecell.
From: |
guix-commits |
Subject: |
02/23: gnu: Add r-hsmmsinglecell. |
Date: |
Tue, 12 Mar 2019 17:48:04 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 557a1089c634198b5aee20afb330f92ec204e876
Author: Ricardo Wurmus <address@hidden>
Date: Tue Mar 12 21:30:47 2019 +0100
gnu: Add r-hsmmsinglecell.
* gnu/packages/bioconductor.scm (r-hsmmsinglecell): New variable.
---
gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8df065a..329bacb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -33,6 +33,9 @@
#:use-module (gnu packages statistics)
#:use-module (gnu packages web))
+
+;;; Annotations
+
(define-public r-bsgenome-celegans-ucsc-ce6
(package
(name "r-bsgenome-celegans-ucsc-ce6")
@@ -647,6 +650,44 @@ based on the knownGene track.")
(license license:artistic2.0)))
+;;; Experiment data
+
+(define-public r-hsmmsinglecell
+ (package
+ (name "r-hsmmsinglecell")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/experiment/" instead of "bioc/".
+ (uri (string-append "https://www.bioconductor.org/packages/"
+ "release/data/experiment/src/contrib/"
+ "HSMMSingleCell_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
+ (properties
+ `((upstream-name . "HSMMSingleCell")))
+ (build-system r-build-system)
+ (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
+ (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle
myoblasts (HSMM)")
+ (description
+ "Skeletal myoblasts undergo a well-characterized sequence of
+morphological and transcriptional changes during differentiation. In this
+experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
+under high mitogen conditions (GM) and then differentiated by switching to
+low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
+hundred cells taken over a time-course of serum-induced differentiation.
+Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
+72 hours) following serum switch using the Fluidigm C1 microfluidic system.
+RNA from each cell was isolated and used to construct mRNA-Seq libraries,
+which were then sequenced to a depth of ~4 million reads per library,
+resulting in a complete gene expression profile for each cell.")
+ (license license:artistic2.0)))
+
+
+;;; Packages
+
(define-public r-biocgenerics
(package
(name "r-biocgenerics")
- 15/23: gnu: Add r-minpack-lm., (continued)
- 15/23: gnu: Add r-minpack-lm., guix-commits, 2019/03/12
- 09/23: gnu: Add r-tensora., guix-commits, 2019/03/12
- 06/23: gnu: Add r-upsetr., guix-commits, 2019/03/12
- 10/23: gnu: Add r-rarpack., guix-commits, 2019/03/12
- 05/23: gnu: Add r-blockmodeling., guix-commits, 2019/03/12
- 14/23: gnu: Add r-gamlss-dist., guix-commits, 2019/03/12
- 12/23: gnu: Add r-cobs., guix-commits, 2019/03/12
- 08/23: gnu: Add r-bayesm., guix-commits, 2019/03/12
- 07/23: gnu: Add r-outliers., guix-commits, 2019/03/12
- 04/23: gnu: Add r-dorng., guix-commits, 2019/03/12
- 02/23: gnu: Add r-hsmmsinglecell.,
guix-commits <=
- 03/23: gnu: r-qvalue: Move to (gnu packages bioconductor)., guix-commits, 2019/03/12
- 01/23: gnu: Add guile-persist., guix-commits, 2019/03/12