snapCGH

DOI: 10.18129/B9.bioc.snapCGH    

This package is for version 3.9 of Bioconductor; for the 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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	Segmentation Overview
PDF		Reference Manual

Details

biocViews	CopyNumberVariation, Microarray, Preprocessing, Software, TwoChannel
Version	1.54.0
In Bioconductor since	BioC 1.8 (R-2.3) (13.5 years)
License	GPL
Depends	limma, DNAcopy, methods
Imports	aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma, methods, stats, tilingArray, utils
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	ADaCGH2
Suggests Me	beadarraySNP
Links To Me
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
Package Short Url	https://bioconductor.org/packages/snapCGH/
Package Downloads Report	Download Stats