genoset

DOI: 10.18129/B9.bioc.genoset    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see genoset.

A RangedSummarizedExperiment with methods for copy number analysis

Bioconductor version: 3.9

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 (version "3.6") and enter:

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

BiocManager::install("genoset")

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("genoset")

 

HTML	R Script	genoset
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, DataRepresentation, Infrastructure, Microarray, SNP, Software
Version	1.40.0
In Bioconductor since	BioC 2.8 (R-2.13) (8.5 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	testthat, 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
Links To Me
Build Report

Package Archives

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

Source Package	genoset_1.40.0.tar.gz
Windows Binary	genoset_1.40.0.zip
Mac OS X 10.11 (El Capitan)	genoset_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/genoset
Source Repository (Developer Access)	git clone [email protected]:packages/genoset
Package Short Url	https://bioconductor.org/packages/genoset/
Package Downloads Report	Download Stats