source("http://bioconductor.org/biocLite.R")
biocLite("crlmm")

crlmm

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

Bioconductor version: 2.13

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.Carvalho at cancer.org.uk>, Robert Scharpf <rscharpf at jhsph.edu>, Matt Ritchie <mritchie at wehi.EDU.AU>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("crlmm")

Documentation

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

browseVignettes("crlmm")

 

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

Details

biocViews	Bioinformatics, CopyNumberVariants, Microarray, Preprocessing, SNP, Software
Version	1.20.4
In Bioconductor since	BioC 2.4 (R-2.9)
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
Suggests	hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.7), GGdata, snpStats, ellipse, RUnit, VGAM
System Requirements
URL
Depends On Me
Imports Me
Suggests Me	ArrayTV, hapmap370k, oligoClasses, SNPchip

Package Archives

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

Package Source	crlmm_1.20.4.tar.gz
Windows Binary	crlmm_1.20.4.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	crlmm_1.20.4.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats