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Bioconductor - crlmm (development version)

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 (3.22)

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 "4.5") 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 1.67.0 In Bioconductor since BioC 2.4 (R-2.9) (16 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 Package Archives

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

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