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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 (3.19)

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 (from within R, enter 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 PDF
crlmm Vignette - Downstream Analysis PDF
crlmm Vignette - Genotyping PDF R Script
Infrastructure for copy number analysis PDF
Overview of copy number vignettes PDF
Preprocessing and genotyping Illumina arrays for copy number analysis PDF
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, Microarray, Preprocessing, SNP, Software
Version 1.61.0
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, 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 hapmap370k, oligoClasses
Links To Me
Build Report Build Report

Package Archives

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

Source Package crlmm_1.61.0.tar.gz
Windows Binary crlmm_1.61.0.zip
macOS Binary (x86_64) crlmm_1.61.0.tgz
macOS Binary (arm64) crlmm_1.61.0.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