#########################################################################/**
# @RdocPackage aroma.Base
#
# \encoding{latin1}
#
# \description{
# @eval "getDescription(aroma.Base)". For a reference on BASE, see [1].
# The homepage for BASE is \url{http://base.thep.lu.se/}.
# }
#
# \section{Requirements}{
# This package requires that the \pkg{R.oo} [2] and the \pkg{R.utils} packages are installed. For RSP generated reports, the \pkg{R.rsp} package is required.
# }
#
# \section{Installation}{
# To install this package please see \url{http://www.braju.com/R/}.
# }
#
# \section{To get started}{
# To get started, see:
# \enumerate{
# \item @see "BasePluginDispatcher" - Generic methods to dispatcher
# R plugins for BASE. For plugin writers. The help on
# @see "main.BasePluginDispatcher" is highly recommended and
# explains how aroma.Base optimize memory usage etc.
# \item @see "BaseFile" - Class representing a BASE file structure.
# An instance of this class contains different types of
# @see "BaseFileSection" objects.
# \item See also the code of example plugins that come with this
# package. They are located in
# \code{system.file("plugins", package="aroma.Base")}.
# \item For low-level reading and writing of BASE files, see
# @see "readBaseFile" and @see "writeBaseFile". This is only
# for users how want to write BASE plugins without using the
# BASE plugin dispatcher, which is not recommended.
# }
# }
#
# \section{Additional help}{
# Below is the plugin description for the helloWorld plugin.
# Aditional plugins are available in \code{system.file("plugins", package="aroma.Base")}.
# @eval "{path <- filePath('../inst/plugins/helloWorld'); file <- list.files(pattern='^plugin.*[.]base$', path=path, full.names=TRUE)[1]; text <- readBaseFile(file)$plugin$headers$descr; text <- strsplit(text, split=c('\\\\r\\\\n', '\\\\n', '\\\\r'))[[1]]; text <- gsub('^([^a-z:]*):$', '\\\\bold{\\1}\\\\cr', text); text <- gsub(' [*]([^*]*)[*] ', ' \\\\bold{\\1} ', text); text <- gsub(' _([^_]*)_ ', ' \\\\emph{\\1} ', text); text <- gsub('([^\\\\])([_$])', '\\1\\\\\\2', text); text <- gsub('\\\\!', '!', text); text <- paste(text, collapse='\n'); text; }"
#
# }
#
# \section{How to cite this package}{
# Whenever using this package, for now, please cite [1] as\cr
#
# @howtocite "aroma.Base"
# }
#
# @author
#
# \section{License}{
# The releases of this package is licensed under
# LGPL version 2.1 or newer.
#
# The development code of the packages is under a private licence
# (where applicable) and patches sent to the author fall under the
# latter license, but will be, if incorporated, released under the
# "release" license above.
# }
#
# \references{
# Some of the reference below can be found at
# \url{http://www.maths.lth.se/bioinformatics/publications/}.\cr
#
# [1] L.H. Saal, C. Troein, J. Vallon-Christersson, S. Gruvberger,
# Å. Borg & C. Peterson, \emph{BioArray Software Environment (BASE):
# a platform for comprehensive management and analysis of microarray
# data}. Genome Biology, 2002.\cr
#
# [2] @include "../incl/BengtssonH_2003.bib.Rdoc" \cr
#
# [3] H. Bengtsson, \emph{A generic R plugin dispatcher for BASE},
# Poster presented at the MGED8 conference, Bergen, Norway,
# September 2005.\cr
#
# [4] H. Bengtsson, \emph{aroma - An R Object-oriented Microarray
# Analysis environment}, Preprints in Mathematical Sciences (manuscript
# in preparation), Mathematical Statistics, Centre for Mathematical
# Sciences, Lund University, 2004.\cr
#
# [5] @include "../incl/BengtssonH_etal_2004.bib.Rdoc" \cr
#
# [6] @include "../incl/BengtssonHossjer_2006.bib.Rdoc" \cr
#
# }
#*/#########################################################################
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