genoset

DOI: 10.18129/B9.bioc.genoset    

A RangedSummarizedExperiment with methods for copy number analysis

Bioconductor version: Release (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("genoset", version = "3.8")

Documentation

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

browseVignettes("genoset")

 

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Details

biocViews CopyNumberVariation, DataRepresentation, Infrastructure, Microarray, SNP, Software
Version 1.38.0
In Bioconductor since BioC 2.8 (R-2.13) (7.5 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_1.38.0.tar.gz
Windows Binary genoset_1.38.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) genoset_1.38.0.tgz
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 http://bioconductor.org/packages/genoset/
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