crlmm

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

Bioconductor version: 2.7

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 <carvalho at bclab.org>, 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 <carvalho at bclab.org>, 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		illumina_copynumber.pdf
PDF		Reference Manual

Details

biocViews	Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants
Depends	R (>= 2.11.0), methods, Biobase(>= 2.9.0), oligoClasses(>= 1.11.7)
Imports	affyio(>= 1.15.2), ellipse, ff, genefilter, mvtnorm, preprocessCore, splines, stats, SNPchip, utils
Suggests	hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.2), snpMatrix, ellipse
System Requirements
License	Artistic-2.0
URL
Depends On Me	VanillaICE
Imports Me
Suggests Me	hapmap370k
Version	1.8.11
Since	Bioconductor 2.4 (R-2.9)

Package Downloads

Package Source	crlmm_1.8.11.tar.gz
Windows Binary	crlmm_1.8.11.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	crlmm_1.8.11.tgz
Package Downloads Report	Download Stats

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