crlmm
This is the development version of crlmm; for the stable 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: Development (3.20)
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 "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.63.0 |
In Bioconductor since | BioC 2.4 (R-2.9) (15.5 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, 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), snpStats, RUnit |
Linking To | preprocessCore(>= 1.17.7) |
Enhances | |
Depends On Me | MAGAR |
Imports Me | VanillaICE |
Suggests Me | oligoClasses, hapmap370k |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | crlmm_1.63.0.tar.gz |
Windows Binary | crlmm_1.63.0.zip |
macOS Binary (x86_64) | crlmm_1.63.0.tgz |
macOS Binary (arm64) | crlmm_1.63.0.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 |