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")

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

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