crlmm

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 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 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
URL
Depends On Me
Imports Me minfi, VanillaICE
Suggests Me hapmap370k, oligoClasses, SNPchip

Package Downloads

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