crlmm
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Bioconductor version: 2.9
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 <Benilton.Carvalho at cancer.org.uk>, Robert Scharpf <rscharpf at jhsph.edu>, Matt Ritchie <mritchie at wehi.edu.au>, Ingo Ruczinski <iruczins at jhsph.edu>, Rafael A Irizarry
Maintainer: Benilton S Carvalho <Benilton.Carvalho at cancer.org.uk>, Robert Scharpf <rscharpf at jhsph.edu>, Matt Ritchie <mritchie at wehi.EDU.AU>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("crlmm")
To cite this package in a publication, start R and enter:
citation("crlmm")
Documentation
| R Script | Copy number estimation | |
| R Script | crlmm Vignette - Downstream Analysis | |
| R Script | crlmm Vignette - Genotyping | |
| crlmmIllumina.pdf | ||
| illumina_copynumber.pdf | ||
| R Script | Infrastructure for copy number analysis | |
| R Script | Overview of copy number vignettes | |
| R Script | Preprocessing and genotyping Affymetrix array for copy number analysis | |
| R Script | Preprocessing and genotyping Illumina arrays for copy number analysis | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants |
| Depends | R (>= 2.13.0), methods, Biobase(>= 2.11.9), oligoClasses(>= 1.15.41) |
| Imports | affyio(>= 1.19.2), ellipse, ff (>= 2.2-1), genefilter(>= 1.33.0), mvtnorm, preprocessCore(>= 1.13.4), splines, stats, SNPchip, utils, lattice |
| Suggests | hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.4), snpStats, ellipse, RUnit, ff |
| System Requirements | |
| License | Artistic-2.0 |
| URL | |
| Depends On Me | |
| Imports Me | minfi |
| Suggests Me | hapmap370k, VanillaICE |
| Version | 1.12.1 |
| Since | Bioconductor 2.4 (R-2.9) |
Package Downloads
| Package Source | crlmm_1.12.1.tar.gz |
| Windows Binary | crlmm_1.12.1.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | crlmm_1.12.1.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Variants
- Flow Cytometry and other assays
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