crlmm

DOI: 10.18129/B9.bioc.crlmm    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see crlmm.

Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Bioconductor version: 3.9

Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.

Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry

Maintainer: Benilton S Carvalho <benilton at unicamp.br>, Robert Scharpf <rscharpf at jhsph.edu>, Matt Ritchie <mritchie at wehi.EDU.AU>

Citation (from within R, enter citation("crlmm")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("crlmm")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("crlmm")

 

PDF Copy number estimation
PDF crlmm Vignette - Downstream Analysis
PDF R Script crlmm Vignette - Genotyping
PDF Infrastructure for copy number analysis
PDF Overview of copy number vignettes
PDF Preprocessing and genotyping Illumina arrays for copy number analysis
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariation, Microarray, Preprocessing, SNP, Software
Version 1.42.0
In Bioconductor since BioC 2.4 (R-2.9) (10.5 years)
License Artistic-2.0
Depends R (>= 2.14.0), oligoClasses(>= 1.21.12), preprocessCore(>= 1.17.7)
Imports methods, Biobase(>= 2.15.4), BiocGenerics, affyio(>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM, parallel, graphics, limma, beanplot
LinkingTo preprocessCore(>= 1.17.7)
Suggests hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.7), GGdata, snpStats, RUnit
SystemRequirements
Enhances
URL
Depends On Me
Imports Me VanillaICE
Suggests Me ArrayTV, hapmap370k, oligoClasses, SNPchip
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package crlmm_1.42.0.tar.gz
Windows Binary crlmm_1.42.0.zip
Mac OS X 10.11 (El Capitan) crlmm_1.42.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/crlmm
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/crlmm
Package Short Url https://bioconductor.org/packages/crlmm/
Package Downloads Report Download Stats

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