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("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 |
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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |