From 25a9a40a12f7476edd81ef0939a40336645c1c46 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Tue, 20 Apr 2021 13:16:59 -0500 Subject: New package: r-missmethyl (#23140) --- .../repos/builtin/packages/r-missmethyl/package.py | 48 ++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-missmethyl/package.py (limited to 'var') 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 index 0000000000..1e1d244dd7 --- /dev/null +++ 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')) -- cgit v1.2.3-70-g09d2