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authorpjotrp2016-09-30 09:25:11 +0000
committerpjotrp2016-09-30 09:25:11 +0000
commitead155ea6347141ffb1279aefb35f5faccff5047 (patch)
treedf2b7a19ed3ff4d32ef1e4624d8cd4fad6ef0da5 /gn
parent8ded2a3ba155f70b495ddcf218fe479b5993f5b4 (diff)
downloadguix-bioinformatics-ead155ea6347141ffb1279aefb35f5faccff5047.tar.gz
R-ctl addedgn-staging
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/genenetwork.scm1
-rw-r--r--gn/packages/statistics.scm28
2 files changed, 28 insertions, 1 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 63e0fb9..dfbba02 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -192,6 +192,7 @@ location of a putative QTL.")
(propagated-inputs `( ;; propagated for development purposes
("python" ,python-2) ;; probably superfluous
("r" ,r)
+ ("r-ctl" ,r-ctl)
("r-wgcna" ,r-wgcna)
("r-qtl" ,r-qtl)
("redis" ,redis)
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index dbe6b99..b83ccf2 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -14,6 +14,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
+ #:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
@@ -333,7 +334,7 @@
(uri (git-reference
(url "https://github.com/genenetwork/pylmm.git")
(commit commit)))
- (file-name (string-append name "-" commit))
+ (file-name (string-append name "-" commit))
(sha256
(base32
"0wryaadb36i275p9d2i1kzflahvbl9kj5wlk8jlbvjij8gpqg964"))))
@@ -362,3 +363,28 @@
(description "Fast and lightweight linear mixed-model (LMM) solver
for use in genome-wide association studies (GWAS).")
(license license:agpl3+))))
+
+(define-public r-ctl
+ (package
+ (name "r-ctl")
+ (version "1.0.0-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/ctl_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "12hrrql9wz43s1d3sfyzlqzx7ajrl3hvf96776ik6icbm8by8h6j"))))
+ (build-system r-build-system)
+ (inputs `(
+ ("r-qtl" ,r-qtl)
+ ))
+ (home-page "https://github.com/DannyArends/CTLmapping")
+ (synopsis "R package for analysis of genetical genomic data to identify genetic loci associated with correlation changes in quantitative traits (CTL)")
+ (description "Analysis of experimental crosses to identify genetic
+markers associated with correlation changes in quantitative
+traits (CTL). The additional correlation information obtained can be
+combined with QTL information to perform de novo reconstruction of
+interaction networks.")
+ (license license:gpl3)))