To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("aCGH")
In most cases, you don't need to download the package archive at all.
aCGH
Classes and functions for Array Comparative Genomic Hybridization data.
Bioconductor version: 3.0
Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.
Author: Jane Fridlyand <jfridlyand at cc.ucsf.edu>, Peter Dimitrov <dimitrov at stat.Berkeley.EDU>
Maintainer: Peter Dimitrov <dimitrov at stat.Berkeley.EDU>
Citation (from within R,
enter citation("aCGH")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("aCGH")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("aCGH")
| R Script | aCGH Overview | |
| Reference Manual |
Details
| biocViews | CopyNumberVariation, DataImport, Genetics, Software |
| Version | 1.44.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier |
| License | GPL-2 |
| Depends | R (>= 2.10), cluster, survival, multtest |
| Imports | Biobase, cluster, grDevices, graphics, methods, multtest, stats, survival, splines, utils |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | CRImage |
| Imports Me | ADaCGH2, snapCGH |
| Suggests Me | beadarraySNP |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | aCGH_1.44.0.tar.gz |
| Windows Binary | aCGH_1.44.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | aCGH_1.44.0.tgz |
| Mac OS X 10.9 (Mavericks) | aCGH_1.44.0.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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