To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("crlmm")
In most cases, you don't need to download the package archive at all.
crlmm
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Bioconductor version: 3.0
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
Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, 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>
Citation (from within R,
enter citation("crlmm")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("crlmm")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("crlmm")
| R Script | Copy number estimation | |
| R Script | crlmm Vignette - Downstream Analysis | |
| R Script | crlmm Vignette - Genotyping | |
| R Script | Infrastructure for copy number analysis | |
| R Script | Overview of copy number vignettes | |
| R Script | Preprocessing and genotyping Illumina arrays for copy number analysis | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, Microarray, Preprocessing, SNP, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) |
| 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, SNPchip, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM, parallel |
| LinkingTo | preprocessCore(>= 1.17.7) |
| Suggests | hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.7), GGdata, snpStats, RUnit |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | VanillaICE |
| Suggests Me | ArrayTV, hapmap370k, SNPchip |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | crlmm_1.24.0.tar.gz |
| Windows Binary | crlmm_1.24.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | crlmm_1.24.0.tgz |
| Mac OS X 10.9 (Mavericks) | crlmm_1.24.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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