crlmm

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

Bioconductor version: 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 <Benilton.Carvalho at cancer.org.uk>, 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 <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 crlmmIllumina.pdf
PDF illumina_copynumber.pdf
PDF R Script Infrastructure for copy number analysis
PDF R Script Preprocessing and genotyping Affymetrix array for copy number analysis
PDF R Script Preprocessing and genotyping Illumina arrays for copy number analysis
PDF   Reference Manual

Details

biocViews Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants
Depends R (>= 2.13.0), methods, Biobase(>= 2.11.9), oligoClasses(>= 1.13.22)
Imports affyio(>= 1.19.2), ellipse, ff (>= 2.2-1), genefilter(>= 1.33.0), mvtnorm, preprocessCore(>= 1.13.4), splines, stats, SNPchip, utils
Suggests hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.4), snpMatrix, ellipse, RUnit
System Requirements
License Artistic-2.0
URL
Depends On Me
Imports Me
Suggests Me hapmap370k
Version 1.10.0
Since Bioconductor 2.4 (R-2.9)

Package Downloads

Package Source crlmm_1.10.0.tar.gz
Windows Binary crlmm_1.10.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary crlmm_1.10.0.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center