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

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DOI: 10.18129/B9.bioc.crlmm

Bioconductor version: Development (3.23)

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 "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumberVariation, Microarray, Preprocessing, SNP, Software

Version 1.69.0

In Bioconductor since BioC 2.4 (R-2.9) (16.5 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

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

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Package Archives

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

Source Package crlmm_1.69.0.tar.gz

Windows Binary (x86_64) crlmm_1.69.0.zip (64-bit only)

macOS Binary (x86_64) crlmm_1.69.0.tgz

macOS Binary (arm64) crlmm_1.69.0.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/

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