\name{available.genomes}

\alias{available.genomes}

\title{available.genomes}

\description{
  Get the list of BSgenome data packages that are currently available on the
  Bioconductor repositories for your version of R/Bioconductor.
}

\usage{
  available.genomes(type=getOption("pkgType"))
}

\arguments{
  \item{type}{
    Character string indicating the type of package (\code{"source"},
    \code{"mac.binary"} or \code{"win.binary"}) to look for.
  }
}

\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 \link{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{H. Pages}

\seealso{
  \link{BSgenome-class},
  \code{\link[utils]{available.packages}}
}

\examples{
  # Get the list of 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
}

\keyword{manip}