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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("snapCGH")
In most cases, you don't need to download the package archive at all.
snapCGH
Segmentation, normalisation and processing of aCGH data.
Bioconductor version: 2.14
Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.
Author: Mike L. Smith, John C. Marioni, Steven McKinney, Thomas Hardcastle, Natalie P. Thorne
Maintainer: John Marioni <marioni at uchicago.edu>
Citation (from within R,
enter citation("snapCGH")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("snapCGH")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("snapCGH")
| R Script | Segmentation Overview | |
| Reference Manual |
Details
| biocViews | CopyNumberVariation, Microarray, Preprocessing, Software, TwoChannel |
| Version | 1.34.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) |
| License | GPL |
| Depends | limma, DNAcopy, methods |
| Imports | aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma, methods, stats, tilingArray, utils |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | ADaCGH2 |
| Suggests Me | beadarraySNP |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | snapCGH_1.34.0.tar.gz |
| Windows Binary | snapCGH_1.34.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | snapCGH_1.34.0.tgz |
| Mac OS X 10.9 (Mavericks) | snapCGH_1.34.0.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
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