[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
05/30: gnu: Add r-ensembldb.
From: |
Ricardo Wurmus |
Subject: |
05/30: gnu: Add r-ensembldb. |
Date: |
Tue, 7 Nov 2017 17:32:54 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit aa30ab5aeebc14376ccc29a68d8b4e4fb8184fca
Author: Ricardo Wurmus <address@hidden>
Date: Tue Nov 7 15:32:35 2017 +0100
gnu: Add r-ensembldb.
* gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
---
gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 227bc34..b6a3aa9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9599,6 +9599,50 @@ filters for manipulating Bioconductor annotation
resources. The filters are
used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
(license license:artistic2.0)))
+(define-public r-ensembldb
+ (package
+ (name "r-ensembldb")
+ (version "2.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ensembldb" version))
+ (sha256
+ (base32
+ "1w0lca3ws5j770bmls91cn93lznvv2pc8s42nybdzz3vdxjvb4m1"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationfilter" ,r-annotationfilter)
+ ("r-annotationhub" ,r-annotationhub)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-curl" ,r-curl)
+ ("r-dbi" ,r-dbi)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/jotsetung/ensembldb")
+ (synopsis "Utilities to create and use Ensembl-based annotation databases")
+ (description
+ "The package provides functions to create and use transcript-centric
+annotation databases/packages. The annotation for the databases are directly
+fetched from Ensembl using their Perl API. The functionality and data is
+similar to that of the TxDb packages from the @code{GenomicFeatures} package,
+but, in addition to retrieve all gene/transcript models and annotations from
+the database, the @code{ensembldb} package also provides a filter framework
+allowing to retrieve annotations for specific entries like genes encoded on a
+chromosome region or transcript models of lincRNA genes.")
+ ;; No version specified
+ (license license:lgpl3+)))
+
(define-public r-qvalue
(package
(name "r-qvalue")
- branch master updated (cd21587 -> 12a24ee), Ricardo Wurmus, 2017/11/07
- 02/30: gnu: Add r-complexheatmap., Ricardo Wurmus, 2017/11/07
- 04/30: gnu: Add r-annotationfilter., Ricardo Wurmus, 2017/11/07
- 01/30: gnu: Add r-genomicfiles., Ricardo Wurmus, 2017/11/07
- 03/30: gnu: Add r-dirichletmultinomial., Ricardo Wurmus, 2017/11/07
- 06/30: gnu: Add r-organismdbi., Ricardo Wurmus, 2017/11/07
- 05/30: gnu: Add r-ensembldb.,
Ricardo Wurmus <=
- 07/30: gnu: Add r-biovizbase., Ricardo Wurmus, 2017/11/07
- 10/30: gnu: Add r-gqtlbase., Ricardo Wurmus, 2017/11/07
- 11/30: gnu: Add r-snpstats., Ricardo Wurmus, 2017/11/07
- 08/30: gnu: Add r-ggbio., Ricardo Wurmus, 2017/11/07
- 09/30: gnu: Add r-gprofiler., Ricardo Wurmus, 2017/11/07
- 16/30: gnu: Add r-mice., Ricardo Wurmus, 2017/11/07
- 26/30: gnu: Add r-rsofia., Ricardo Wurmus, 2017/11/07
- 13/30: gnu: Add r-homo-sapiens., Ricardo Wurmus, 2017/11/07
- 15/30: gnu: Add r-ldblock., Ricardo Wurmus, 2017/11/07
- 12/30: gnu: Add r-org-hs-eg-db., Ricardo Wurmus, 2017/11/07