crlmm
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Bioconductor version: 3.24 · Package version: 1.71.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("crlmm")Details
| Maintainer | Benilton S Carvalho <benilton@unicamp.br>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
| Author | Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry |
| License | Artistic-2.0 |
| Downloads rank | 981 |
| Source branch | devel |
| biocViews | CopyNumberVariation, Microarray, Preprocessing, SNP, Software |
Documentation
- Copy number estimation
- crlmm Vignette - Downstream Analysis
- crlmm Vignette - Genotyping
- Infrastructure for copy number analysis
- Overview of copy number vignettes
- Preprocessing and genotyping Illumina arrays for copy number analysis
Download
Follow the installation instructions to use this package in your R session.
| Source package | crlmm_1.71.0.tar.gz |
| Windows binary (x86_64) | crlmm_1.71.0.zip |
| macOS binary (arm64) | crlmm_1.71.0.tgz |
| macOS binary (x86_64) | crlmm_1.71.0.tgz |
Dependencies
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
LinkingTo: preprocessCore (>= 1.17.7)
Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit
Reverse dependencies
Depends On Me (1): MAGAR
Imports Me (1): VanillaICE
Suggests Me (2): hapmap370k, oligoClasses