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authorGlenn Johnson <glenn-johnson@uiowa.edu>2021-04-20 13:16:59 -0500
committerGitHub <noreply@github.com>2021-04-20 11:16:59 -0700
commit25a9a40a12f7476edd81ef0939a40336645c1c46 (patch)
tree79f0ec5569546257e680275314711251c370354e
parent639d66720f7e3c4224613bbb319633b1969d150a (diff)
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New package: r-missmethyl (#23140)
-rw-r--r--var/spack/repos/builtin/packages/r-missmethyl/package.py48
1 files changed, 48 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-missmethyl/package.py b/var/spack/repos/builtin/packages/r-missmethyl/package.py
new file mode 100644
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+++ b/var/spack/repos/builtin/packages/r-missmethyl/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMissmethyl(RPackage):
+ """Analysing Illumina HumanMethylation BeadChip Data:
+
+ Normalisation, testing for differential variability and differential
+ methylation and gene set testing for data from Illumina's Infinium
+ HumanMethylation arrays. The normalisation procedure is subset-quantile
+ within-array normalisation (SWAN), which allows Infinium I and II type
+ probes on a single array to be normalised together. The test for
+ differential variability is based on an empirical Bayes version of Levene's
+ test. Differential methylation testing is performed using RUV, which can
+ adjust for systematic errors of unknown origin in high-dimensional data by
+ using negative control probes. Gene ontology analysis is performed by
+ taking into account the number of probes per gene on the array, as well as
+ taking into account multi-gene associated probes."""
+
+ bioc = "missMethyl"
+
+ version('1.24.0', commit='f6c86048911dc0e302fb593b7d0623f6e77ac332')
+
+ depends_on('r@3.6.0:', type=('build', 'run'))
+ depends_on('r-illuminahumanmethylation450kanno-ilmn12-hg19', type=('build', 'run'))
+ depends_on('r-illuminahumanmethylationepicanno-ilm10b4-hg19', type=('build', 'run'))
+ depends_on('r-annotationdbi', type=('build', 'run'))
+ depends_on('r-biasedurn', type=('build', 'run'))
+ depends_on('r-biobase', type=('build', 'run'))
+ depends_on('r-biocgenerics', type=('build', 'run'))
+ depends_on('r-genomicranges', type=('build', 'run'))
+ depends_on('r-go-db', type=('build', 'run'))
+ depends_on('r-illuminahumanmethylation450kmanifest', type=('build', 'run'))
+ depends_on('r-illuminahumanmethylationepicmanifest', type=('build', 'run'))
+ depends_on('r-iranges', type=('build', 'run'))
+ depends_on('r-limma', type=('build', 'run'))
+ depends_on('r-methylumi', type=('build', 'run'))
+ depends_on('r-minfi', type=('build', 'run'))
+ depends_on('r-org-hs-eg-db', type=('build', 'run'))
+ depends_on('r-ruv', type=('build', 'run'))
+ depends_on('r-s4vectors', type=('build', 'run'))
+ depends_on('r-statmod', type=('build', 'run'))
+ depends_on('r-stringr', type=('build', 'run'))
+ depends_on('r-summarizedexperiment', type=('build', 'run'))