available.genomes {BSgenome}R Documentation

available.genomes

Description

Gets the list of Biostrings-based genome data packages (aka the BSgenome data packages) currently available.

Usage

  available.genomes()

Details

A BSgenome data package contains the full genome for a given organism. Its name has 4 parts separated by a dot (e.g. BSgenome.Celegans.UCSC.ce2). The 1st part is always BSgenome, the 2nd part is the name of the organism (abbreviated), the 3rd part is the name of the organisation who assembled the genome and the 4th part is the release string or number used by this organisation for this genome. A BSgenome data package contains a single BSgenome object named like the second part of the package name (e.g. Celegans in the case of BSgenome.Celegans.UCSC.ce2) where all the sequences for this genome are stored.

Value

A character vector containing the names of the BSgenome data packages currently available.

Author(s)

H. Pages

See Also

BSgenome-class

Examples

  # Look at the BSgenome data packages currently available:
  available.genomes()

  # Make your choice and install with:
  source("http://bioconductor.org/biocLite.R")
  biocLite("BSgenome.Celegans.UCSC.ce2")

  # Have a coffee ;-)

  # Load the package and display the index of sequences for this genome:
  library(BSgenome.Celegans.UCSC.ce2)
  Celegans

[Package BSgenome version 1.6.2 Index]