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("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 | ||
| 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 |