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* [bug#56161] [PATCH] gnu: Add r-atena.
@ 2022-06-23 10:25 Mădălin Ionel Patrașcu
  0 siblings, 0 replies; only message in thread
From: Mădălin Ionel Patrașcu @ 2022-06-23 10:25 UTC (permalink / raw)
  To: 56161

* gnu/packages/bioconductor.scm (r-atena): 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 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





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