DOI: 10.18129/B9.bioc.crlmm    

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

Bioconductor version: Release (3.6)

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 at>, Robert Scharpf <rscharpf at>, Matt Ritchie <mritchie at wehi.EDU.AU>

Citation (from within R, enter citation("crlmm")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


To view documentation for the version of this package installed in your system, start R and enter:



PDF Copy number estimation
PDF crlmm Vignette - Downstream Analysis
PDF R Script crlmm Vignette - Genotyping
PDF Infrastructure for copy number analysis
PDF Overview of copy number vignettes
PDF Preprocessing and genotyping Illumina arrays for copy number analysis
PDF   Reference Manual
Text   NEWS


biocViews CopyNumberVariation, Microarray, Preprocessing, SNP, Software
Version 1.36.0
In Bioconductor since BioC 2.4 (R-2.9) (9 years)
License Artistic-2.0
Depends R (>= 2.14.0), oligoClasses(>= 1.21.12), preprocessCore(>= 1.17.7)
Imports methods, Biobase(>= 2.15.4), BiocGenerics, affyio(>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip, utils, lattice, ff, foreach, RcppEigen (>=, matrixStats, VGAM, parallel, graphics, limma, beanplot
LinkingTo preprocessCore(>= 1.17.7)
Suggests hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.7), GGdata, snpStats, RUnit
Depends On Me
Imports Me VanillaICE
Suggests Me ArrayTV, hapmap370k, oligoClasses, SNPchip
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package crlmm_1.36.0.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) crlmm_1.36.0.tgz
Source Repository git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: