- Home
- Bioconductor 3.0
- Software Packages
- genoset
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("genoset")
In most cases, you don't need to download the package archive at all.
genoset
Provides classes similar to ExpressionSet for copy number analysis
Bioconductor version: 3.0
Load, manipulate, and plot copynumber and BAF data. GenoSet class extends eSet by adding a "locData" slot for a GRanges object. This object contains feature genome location data and provides for efficient subsetting on genome location. Provides convenience functions for processing of copy number and B-Allele Frequency data. Provides the class RleDataFrame to store runs of data along the genome for multiple samples.
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:
source("http://bioconductor.org/biocLite.R")
biocLite("genoset")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("genoset")
| R Script | genoset | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, DataRepresentation, Infrastructure, Microarray, SNP, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), BiocGenerics(>= 0.11.3), Biobase(>= 2.15.1), GenomicRanges(>= 1.17.19) |
| Imports | S4Vectors(>= 0.2.3), GenomeInfoDb(>= 1.1.3), IRanges, methods, graphics |
| LinkingTo | |
| Suggests | RUnit, DNAcopy, stats, BSgenome, Biostrings |
| SystemRequirements | |
| Enhances | parallel |
| URL | https://github.com/phaverty/genoset |
| Depends On Me | VegaMC |
| Imports Me | methyAnalysis |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | genoset_1.20.0.tar.gz |
| Windows Binary | genoset_1.20.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | genoset_1.20.0.tgz |
| Mac OS X 10.9 (Mavericks) | genoset_1.20.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2015, Bioconductor
