crlmm

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

Bioconductor version: 2.5

Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 6.0.

Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh at jhsph.edu>, Robert Scharpf <rscharpf at jhsph.edu>, Matt Ritchie <mritchie at wehi.EDU.AU>

Maintainer: Benilton S Carvalho <bcarvalh at jhsph.edu>, 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	crlmm Vignette - Copy Number
PDF	R Script	crlmm Vignette - Downstream Analysis
PDF	R Script	crlmm Vignette - Genotyping
PDF		crlmmIllumina.pdf
PDF		Reference Manual

Details

biocViews	Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants
Depends	methods, Biobase(>= 2.5.5), R (>= 2.10.0)
Imports	affyio, preprocessCore, utils, stats, genefilter, splines, mvtnorm, oligoClasses, ellipse, methods, SNPchip
Suggests	hapmapsnp5, hapmapsnp6, genomewidesnp5Crlmm(>= 1.0.2), genomewidesnp6Crlmm(>= 1.0.2), snpMatrix, VanillaICE(>= 1.7.8), GGdata
System Requirements
License	Artistic-2.0
URL
Depends On Me
Imports Me
Suggests Me
Version	1.4.5
Since	Bioconductor 2.4 (R-2.9)

Package Downloads

Package Source	crlmm_1.4.5.tar.gz
Windows Binary	crlmm_1.4.5.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	crlmm_1.4.5.tgz
Package Downloads Report	Download Stats

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