genoset

DOI: 10.18129/B9.bioc.genoset    

A RangedSummarizedExperiment with methods for copy number analysis

Bioconductor version: Release (3.6)

GenoSet provides an extension of the RangedSummarizedExperiment class with additional API features. This class provides convenient and fast methods for working with segmented genomic data. Additionally, GenoSet provides the class RleDataFrame which stores runs of data along the genome for multiple samples and provides very fast summaries of arbitrary row sets (regions of the genome).

Author: Peter M. Haverty

Maintainer: Peter M. Haverty <phaverty at gene.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("genoset")

Documentation

HTML	R Script	genoset
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, DataRepresentation, Infrastructure, Microarray, SNP, Software
Version	1.34.0
In Bioconductor since	BioC 2.8 (R-2.13) (7 years)
License	Artistic-2.0
Depends	R (>= 2.10), BiocGenerics(>= 0.11.3), GenomicRanges(>= 1.17.19), SummarizedExperiment(>= 1.1.6)
Imports	S4Vectors(>= 0.13.13), GenomeInfoDb(>= 1.1.3), IRanges(>= 2.5.12), methods, graphics
LinkingTo
Suggests	RUnit, knitr, BiocStyle, rmarkdown, DNAcopy, stats, BSgenome, Biostrings
SystemRequirements
Enhances	parallel
URL	https://github.com/phaverty/genoset
Depends On Me
Imports Me	methyAnalysis, VegaMC
Suggests Me
Build Report

Package Archives

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

Source Package	genoset_1.34.0.tar.gz
Windows Binary	genoset_1.34.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	genoset_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/genoset
Package Short Url	http://bioconductor.org/packages/genoset/
Package Downloads Report	Download Stats