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>

Citation (from within R, enter citation("genoset")):

Installation

To install this package, start R (version "4.1") and enter:


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

BiocManager::install("genoset")

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

Documentation

Reference Manual PDF

Details

biocViews CopyNumberVariation, DataRepresentation, Infrastructure, Microarray, SNP, Software
Version 1.48.0
In Bioconductor since BioC 2.8 (R-2.13) (13 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
System Requirements
URL https://github.com/phaverty/genoset
See More
Suggests testthat, knitr, BiocStyle, rmarkdown, DNAcopy, stats, BSgenome, Biostrings
Linking To
Enhances parallel
Depends On Me
Imports Me methyAnalysis
Suggests Me
Links To Me
Build Report 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/
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Old Source Packages for BioC 3.13 Source Archive