crlmm
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see crlmm.
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Bioconductor version: 3.9
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 unicamp.br>, Robert Scharpf <rscharpf at jhsph.edu>, Matt Ritchie <mritchie at wehi.EDU.AU>
citation("crlmm")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("crlmm")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("crlmm")| Copy number estimation | ||
| crlmm Vignette - Downstream Analysis | ||
| crlmm Vignette - Genotyping | R Script | |
| Infrastructure for copy number analysis | ||
| Overview of copy number vignettes | ||
| Preprocessing and genotyping Illumina arrays for copy number analysis | ||
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Microarray, Preprocessing, SNP, Software |
| Version | 1.42.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (15 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, graphics, limma, beanplot |
| System Requirements | |
| URL |
See More
| Suggests | hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.7), GGdata, snpStats, RUnit |
| Linking To | preprocessCore(>= 1.17.7) |
| Enhances | |
| Depends On Me | |
| Imports Me | VanillaICE |
| Suggests Me | ArrayTV, hapmap370k, oligoClasses, SNPchip |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | crlmm_1.42.0.tar.gz |
| Windows Binary | crlmm_1.42.0.zip |
| Mac OS X 10.11 (El Capitan) | crlmm_1.42.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/crlmm |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/crlmm |
| Bioc Package Browser | https://code.bioconductor.org/browse/crlmm/ |
| Package Short Url | https://bioconductor.org/packages/crlmm/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |