To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("crlmm")

In most cases, you don't need to download the package archive at all.

crlmm

This package is for version 2.8 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: 2.8

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 <Benilton.Carvalho at cancer.org.uk>, Robert Scharpf <rscharpf at jhsph.edu>, Matt Ritchie <mritchie at wehi.edu.au>, Ingo Ruczinski <iruczins at jhsph.edu>, 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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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		AffymetrixPreprocessCN.pdf
PDF		copynumber.pdf
PDF		crlmmDownstream.pdf
PDF		crlmmIllumina.pdf
PDF		illumina_copynumber.pdf
PDF		IlluminaPreprocessCN.pdf
PDF		Infrastructure.pdf
PDF		Reference Manual

Details

biocViews	Bioinformatics, CopyNumberVariants, Microarray, Preprocessing, SNP, Software
Version	1.10.0
In Bioconductor since	BioC 2.4 (R-2.9) (7 years)
License	Artistic-2.0
Depends	R (>= 2.13.0), methods, Biobase(>= 2.11.9), oligoClasses(>= 1.13.22)
Imports	affyio(>= 1.19.2), ellipse, ff (>= 2.2-1), genefilter(>= 1.33.0), mvtnorm, preprocessCore(>= 1.13.4), splines, stats, SNPchip, utils
LinkingTo
Suggests	hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.4), snpMatrix, ellipse, RUnit
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	hapmap370k
Build Report

Package Archives

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

Package Source	crlmm_1.10.0.tar.gz
Windows Binary	crlmm_1.10.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/crlmm/tree/release-2.8
Package Short Url	http://bioconductor.org/packages/crlmm/
Package Downloads Report	Download Stats