diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8df065a60c..329bacb190 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") |