Mădălin Ionel Patrașcu wrote 3 years ago
(address . guix-patches@gnu.org)
20220623102520.24412-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-atena): New variable.
---
gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
Toggle diff (56 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1e87b190c2..5ec69365d1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2029,6 +2029,47 @@ (define-public r-aneufinder
sequencing data.")
(license license:artistic2.0)))
+(define-public r-atena
+ (package
+ (name "r-atena")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "atena" version))
+ (sha256
+ (base32
+ "1jbnlxrk8npflym008cgrazamlsh6y624g1d6x648kcjd8zwvj6n"))))
+ (properties `((upstream-name . "atena")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-annotationhub
+ r-biocgenerics
+ r-biocparallel
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-iranges
+ r-matrix
+ r-rsamtools
+ r-s4vectors
+ r-scales
+ r-sparsematrixstats
+ r-squarem
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/functionalgenomics/atena")
+ (synopsis "Analysis of transposable elements")
+ (description
+ "The @code{atena} package quantifies expression of @dfn{TEs} (transposable
+elements) from RNA-seq data through different methods, including @code{ERVmap},
+@code{TEtranscripts} and @code{Telescope}. A common interface is provided to
+use each of these methods, which consists of building a parameter object, calling
+the quantification function with this object and getting a
+@code{SummarizedExperiment} object as an output container of the quantified
+expression profiles. The implementation allows quantifing TEs and gene
+transcripts in an integrated manner.")
+ (license license:artistic2.0)))
+
(define-public r-biocversion
(package
(name "r-biocversion")
base-commit: e74fa406e1043547242a8b67ab9907fea7aae6b9
--
2.36.1