To install this package, start R and enter:
## try http if https is not available source("https://bioconductor.org/biocLite.R") biocLite("crlmm")
In most cases, you don't need to download the package archive at all.
Bioconductor version: Release (3.1)
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>
Citation (from within R,
enter citation("crlmm")
):
To install this package, start R and enter:
## try http if https is not available source("https://bioconductor.org/biocLite.R") biocLite("crlmm")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("crlmm")
R Script | Copy number estimation | |
R Script | crlmm Vignette - Downstream Analysis | |
R Script | crlmm Vignette - Genotyping | |
R Script | Infrastructure for copy number analysis | |
R Script | Overview of copy number vignettes | |
R Script | Preprocessing and genotyping Illumina arrays for copy number analysis | |
Reference Manual | ||
Text | NEWS |
biocViews | CopyNumberVariation, Microarray, Preprocessing, SNP, Software |
Version | 1.26.0 |
In Bioconductor since | BioC 2.4 (R-2.9) (6.5 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 (>= 0.3.1.2.1), matrixStats, VGAM, parallel |
LinkingTo | preprocessCore(>= 1.17.7) |
Suggests | hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.7), GGdata, snpStats, RUnit |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | VanillaICE |
Suggests Me | ArrayTV, hapmap370k, oligoClasses, SNPchip |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | crlmm_1.26.0.tar.gz |
Windows Binary | crlmm_1.26.0.zip (32- & 64-bit) |
Mac OS X 10.6 (Snow Leopard) | crlmm_1.26.0.tgz |
Mac OS X 10.9 (Mavericks) | crlmm_1.26.0.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/crlmm/tree/release-3.1 |
Package Short Url | http://bioconductor.org/packages/crlmm/ |
Package Downloads Report | Download Stats |
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