crlmm
This is the released version of crlmm; for the devel version, see crlmm.
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Bioconductor version: Release (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("crlmm")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.70.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (17.5 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_1.70.0.tar.gz |
| Windows Binary (x86_64) | crlmm_1.70.0.zip |
| macOS Binary (big-sur-x86_64) | crlmm_1.70.0.tgz |
| macOS Binary (sonoma-arm64) | crlmm_1.70.0.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 |