genoset

This package is for version 3.9 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: 3.9

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>

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

Installation

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("genoset")
genoset HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, DataRepresentation, Infrastructure, Microarray, SNP, Software
Version 1.40.0
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(>= 0.13.13), 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, VegaMC
Suggests Me
Links To Me
Build Report 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 git@git.bioconductor.org:packages/genoset
Bioc Package Browser https://code.bioconductor.org/browse/genoset/
Package Short Url https://bioconductor.org/packages/genoset/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive