02/10: gnu: Add r-rtcga.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit 3e203183f85c1b957d90820202aa104cd757dbd3
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Mon Aug 28 17:23:18 2023 +0200

    gnu: Add r-rtcga.
    
    * gnu/packages/bioconductor.scm (r-rtcga): New variable.
---
 gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a864bc91e9..4460b67fb8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9081,6 +9081,51 @@ tab-delimited (tabix) files.")
      "This package models a RESTful service as if it were a nested R list.")
     (license license:artistic2.0)))
 
+(define-public r-rtcga
+  (package
+    (name "r-rtcga")
+    (version "1.30.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "RTCGA" version))
+              (sha256
+               (base32
+                "1y7ciq1270dc1c9y490fygrsylyzwl52fqi1vj7r75hy3rnwnv25"))))
+    (properties `((upstream-name . "RTCGA")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-assertthat
+                             r-data-table
+                             r-dplyr
+                             r-ggplot2
+                             r-ggthemes
+                             r-htmltools
+                             r-knitr
+                             r-purrr
+                             r-rcurl
+                             r-rmarkdown
+                             r-rvest
+                             r-scales
+                             r-stringi
+                             r-survival
+                             r-survminer
+                             r-viridis
+                             r-xml
+                             r-xml2))
+    (native-inputs (list r-knitr))
+    (home-page "https://rtcga.github.io/RTCGA/";)
+    (synopsis "The Cancer Genome Atlas data integration")
+    (description
+     "The Cancer Genome Atlas (TCGA) Data Portal provides a platform for
+researchers to search, download, and analyze data sets generated by TCGA.  It
+contains clinical information, genomic characterization data, and high level
+sequence analysis of the tumor genomes.  The key is to understand genomics to
+improve cancer care.  RTCGA package offers download and integration of the
+variety and volume of TCGA data using patient barcode key, what enables easier
+data possession.  This may have an benefcial infuence on impact on development
+of science and improvement of patients treatment.  Furthermore, RTCGA package
+transforms TCGA data to tidy form which is convenient to use.")
+    (license license:gpl2)))
+
 (define-public r-rtcgatoolbox
   (package
     (name "r-rtcgatoolbox")