Mădălin Ionel Patrașcu wrote 3 years ago
(address . guix-patches@gnu.org)
20220413120442.28226-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-ace): New variable.
---
gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
Toggle diff (42 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 803437a033..ffa442ee1b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11642,6 +11642,35 @@ (define-public r-universalmotif
motifs, and others.")
(license license:gpl3)))
+(define-public r-ace
+ (package
+ (name "r-ace")
+ (version "1.12.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ACE" version))
+ (sha256
+ (base32
+ "1nkbxldn5ba4fzfh4skwjc37gm6apwp09vzwnj2jw3b7ivmr0yr6"))))
+ (properties `((upstream-name . "ACE")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/tgac-vumc/ACE")
+ (synopsis
+ "Absolute copy number estimation from low-coverage whole genome sequencing")
+ (description
+ "This package uses segmented copy number data to estimate tumor cell
+percentage and produce copy number plots displaying absolute copy numbers. For
+this it uses segmented data from the @code{QDNAseq} package, which in turn uses
+a number of dependencies to turn mapped reads into segmented data. @code{ACE}
+will run @code{QDNAseq} or use its output rds-file of segmented data. It will
+subsequently run through all samples in the object(s), for which it will create
+individual subdirectories. For each sample, it will calculate how well the
+segments fit (the relative error) to integer copy numbers for each percentage
+of @dfn{tumor cells} (cells with divergent segments).")
+ (license license:gpl2)))
+
;; This is a CRAN package, but it depends on Bioconductor packages, so we put
;; it here.
(define-public r-activedriverwgs
--
2.34.0