snapCGH

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see snapCGH.

Segmentation, normalisation and processing of aCGH data.


Bioconductor version: 3.9

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 (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("snapCGH")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("snapCGH")
Segmentation Overview PDF R Script
Reference Manual PDF

Details

biocViews CopyNumberVariation, Microarray, Preprocessing, Software, TwoChannel
Version 1.54.0
In Bioconductor since BioC 1.8 (R-2.3) (18 years)
License GPL
Depends limma, DNAcopy, methods
Imports aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma, methods, stats, tilingArray, utils
System Requirements
URL
See More
Suggests
Linking To
Enhances
Depends On Me
Imports Me ADaCGH2
Suggests Me beadarraySNP
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package snapCGH_1.54.0.tar.gz
Windows Binary snapCGH_1.54.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) snapCGH_1.54.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/snapCGH
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/snapCGH
Bioc Package Browser https://code.bioconductor.org/browse/snapCGH/
Package Short Url https://bioconductor.org/packages/snapCGH/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive