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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CGHbase")
In most cases, you don't need to download the package archive at all.
CGHbase
CGHbase: Base functions and classes for arrayCGH data analysis.
Bioconductor version: 3.0
Contains functions and classes that are needed by arrayCGH packages.
Author: Sjoerd Vosse, Mark van de Wiel
Maintainer: Mark van de Wiel <mark.vdwiel at vumc.nl>
Citation (from within R,
enter citation("CGHbase")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CGHbase")
Documentation
| Reference Manual |
Details
| biocViews | CopyNumberVariation, Infrastructure, Microarray, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 2.3 (R-2.8) |
| License | GPL |
| Depends | R (>= 2.10), methods, Biobase(>= 2.5.5), marray |
| Imports | |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | CGHcall, CGHnormaliter, CGHregions, sigaR |
| Imports Me | CGHnormaliter, plrs, QDNAseq |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | CGHbase_1.26.0.tar.gz |
| Windows Binary | CGHbase_1.26.0.zip |
| Mac OS X 10.6 (Snow Leopard) | CGHbase_1.26.0.tgz |
| Mac OS X 10.9 (Mavericks) | CGHbase_1.26.0.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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