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

Bioconductor version: Release (2.11)

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>, Robert Scharpf <rscharpf at>, Matt Ritchie <mritchie at wehi.EDU.AU>

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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


biocViews Bioinformatics, CopyNumberVariants, Microarray, Preprocessing, SNP, Software
Version 1.16.9
In Bioconductor since BioC 2.4 (R-2.9)
License Artistic-2.0
Depends R (>= 2.14.0), oligoClasses(>= 1.19.39), preprocessCore(>= 1.17.7)
Imports methods, Biobase(>= 2.15.4), BiocGenerics, affyio(>= 1.23.2), ellipse, genefilter(>= 1.37.1), mvtnorm, splines, stats, SNPchip, utils, lattice, ff, foreach, RcppEigen
Suggests hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.4), GGdata, snpStats, ellipse, RUnit
System Requirements
Depends On Me
Imports Me minfi, VanillaICE
Suggests Me hapmap370k, oligoClasses, SNPchip

Package Downloads

Package Source crlmm_1.16.9.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) crlmm_1.16.9.tgz
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