%\VignetteIndexEntry{Sequence analysis}
%\VignettePackage{EMBL2011}

\documentclass{article}

\usepackage{BioconductorVignette}

\title{An introduction to \R{} and \Bioconductor{}}
\author{Martin
  Morgan\footnote{\href{mailto:mtmorgan@fhcrc.org}{mtmorgan@fhcrc.org}}}
\date{June 20-23, 2011}

\SweaveOpts{keep.source=TRUE}

\begin{document}

\maketitle

Introduction
- overall work flows

\section{Packages}

\section{Data structures}

\subsection{High-level}
- \Rclass{ShortReadQ}
- \Rclass{GappedAlignments}
- \Rclass{SummarizedExperiment}
- \Rclass{TranscriptDb}

\subsection{Building blocks}
- \Rclass{IRanges}
- \Rclass{GRanges}
- \Rclass{IRangesList}, \Rclass{GRangesList}, \Rclass{RangedData}
- \Rclass{Rle}
- \Rclass{DataFrame}

\subsection{Unifying concepts}
- \Rfunction{metadata} and \Rfunction{elementMetadata}

\section{Work flows}

\subsection{Quality assessment}

Overall
- assessment
- remediation

Domain-specific
- example: microbiome demultiplex, de-barcode, filter

\subsection{RNA-seq}

counting / estimation
differential representation
annotation
down-stream analysis

\subsection{ChIP-seq}

islands
annotation
down-stream analysis

\subsection{\ldots}

\end{document}