genoset

This package is for version 3.10 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

DOI: 10.18129/B9.bioc.genoset

Bioconductor version: 3.10

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumberVariation, DataRepresentation, Infrastructure, Microarray, SNP, Software

Version 1.42.0

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(>= 0.23.18), GenomeInfoDb(>= 1.1.3), IRanges(>= 2.5.12), methods, graphics

System Requirements

URL https://github.com/phaverty/genoset

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_1.42.0.tar.gz

Windows Binary genoset_1.42.0.zip

Mac OS X 10.11 (El Capitan) genoset_1.42.0.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 3.10 Source Archive