03/03: gnu: Add r-amplican.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit 5fb5af5658b7575a945579a7cf51c193600b76bb
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Mon Dec 5 18:27:26 2022 +0100

    gnu: Add r-amplican.
    
    * gnu/packages/bioconductor.scm (r-amplican): New variable.
---
 gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 07f8f658f4..85c07605ca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2202,6 +2202,53 @@ conditions or various species.  @code{AMOUNTAIN} aims to 
search active modules
 in multi-layer WGCN using a continuous optimization approach.")
     (license license:gpl2+)))
 
+(define-public r-amplican
+  (package
+    (name "r-amplican")
+    (version "1.20.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "amplican" version))
+              (sha256
+               (base32
+                "1c990i6gxbarcpbdpkz017x94spwzap95l95synlizbkyif4z8ij"))))
+    (properties `((upstream-name . "amplican")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-clustercrit
+           r-data-table
+           r-dplyr
+           r-genomeinfodb
+           r-genomicranges
+           r-ggplot2
+           r-ggthemes
+           r-gridextra
+           r-gtable
+           r-iranges
+           r-knitr
+           r-matrix
+           r-matrixstats
+           r-rcpp
+           r-rmarkdown
+           r-s4vectors
+           r-shortread
+           r-stringr
+           r-waffle))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/valenlab/amplican";)
+    (synopsis "Automated analysis of CRISPR experiments")
+    (description
+     "The package performs alignment of the amplicon reads, normalizes
+gathered data, calculates multiple statistics (e.g. cut rates, frameshifts)
+and presents the results in the form of aggregated reports.  Data and
+statistics can be broken down by experiments, barcodes, user defined groups,
+guides and amplicons allowing for quick identification of potential
+problems.")
+    (license license:gpl3)))
+
 (define-public r-amaretto
   (package
     (name "r-amaretto")