crlmm

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

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("crlmm")

Documentation

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 CopyNumberVariation, Microarray, Preprocessing, SNP, Software
Version 1.22.0
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, RUnit
System Requirements
URL
Depends On Me
Imports Me
Suggests Me ArrayTV, hapmap370k, oligoClasses, SNPchip

Package Downloads

Package Source crlmm_1.22.0.tar.gz
Windows Binary crlmm_1.22.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) crlmm_1.22.0.tgz
Mac OS X 10.9 (Mavericks)
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