crlmm

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

Bioconductor version: Development (2.8)

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 , Robert Scharpf , Matt Ritchie

To install this package, start R and enter:

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

Documentation

PDF	R Script	Copy number estimation
PDF	R Script	crlmm Vignette - Downstream Analysis
PDF	R Script	crlmm Vignette - Genotyping
PDF		crlmmIllumina.pdf
PDF		illumina_copynumber.pdf
PDF	R Script	Infrastructure for copy number analysis
PDF	R Script	Overview of copy number vignettes
PDF	R Script	Preprocessing and genotyping Affymetrix array for copy number analysis
PDF	R Script	Preprocessing and genotyping Illumina arrays for copy number analysis

Reference Manual

Details

biocViews	Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants
Depends	R, methods, Biobase, oligoClasses
Imports	affyio, ellipse, ff, genefilter, mvtnorm, preprocessCore, splines, stats, SNPchip, utils
Suggests	hapmapsnp6, genomewidesnp6Crlmm, snpMatrix, ellipse, RUnit
System Requirements
License	Artistic-2.0
URL
Depends On Me
Imports Me
Suggests Me
Version	1.9.27

Package Downloads

Package Source	crlmm_1.9.27.tar.gz
Windows Binary	crlmm_1.9.19.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	crlmm_1.9.19.tgz
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