genoset

DOI: 10.18129/B9.bioc.genoset    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see genoset.

A RangedSummarizedExperiment with methods for copy number analysis

Bioconductor version: 3.13

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 "4.1") 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

PDF		Reference Manual

Details

biocViews	CopyNumberVariation, DataRepresentation, Infrastructure, Microarray, SNP, Software
Version	1.48.0
In Bioconductor since	BioC 2.8 (R-2.13) (10.5 years)
License	Artistic-2.0
Depends	R (>= 2.10), BiocGenerics(>= 0.11.3), GenomicRanges(>= 1.17.19), SummarizedExperiment(>= 1.1.6)
Imports	S4Vectors(>= 0.27.3), 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
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/genoset
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/genoset
Package Short Url	https://bioconductor.org/packages/genoset/
Package Downloads Report	Download Stats