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

\documentclass[usenames,dvipsnames]{beamer}

\usepackage{BioconductorSlides}
\hypersetup{colorlinks=true, linkcolor=Blue, urlcolor=Blue,
  citecolor=Blue}

\title{Working with Sequence Data} 

\author{Martin
  Morgan\footnote{\href{mailto:mtmorgan@fhcrc.org}{mtmorgan@fhcrc.org}}}
\date{June 20-23, 2011}

\SweaveOpts{eval=FALSE}

\begin{document}

\maketitle

\begin{frame}{Useful data structures}
  \Biocpkg{IRanges}
  \begin{itemize}
  \item \Rclass{IRanges} / \Rclass{IRangesList} /
    \Rclass{RangedData}-- ranges
  \item \Rclass{Rle} -- run length encoding
  \item \Rclass{Views}
  \end{itemize}
  \Biocpkg{GenomicRanges}
  \begin{itemize}
  \item \Rclass{GRanges} / \Rclass{GRangesList} -- sequence, strand
  \item \Rclass{GappedAlignments} -- CIGAR
  \end{itemize}
  \Biocpkg{Biostrings}, \Biocpkg{BSgenome}
  \begin{itemize}
  \item \Rclass{XString}, \Rclass{XStringSet}
  \end{itemize}
\end{frame}

\begin{frame}{Common work flows}
  Input / output
  \begin{itemize}
  \item Fasta, fastq
  \item SAM / BAM, tabix, indexed fasta -- \Biocpkg{Rsamtools}
  \item Genome tracks \& related formats -- \Biocpkg{rtracklayer}
  \end{itemize}
  Pre-processing / manipulation / count \& measure
  \begin{itemize}
  \item String manipulation, pattern matching
  \item Quality assessment \Biocpkg{ShortRead}
  \item finding / counting overlaps
  \end{itemize}
  Analysis domains
  \begin{itemize}
  \item ChIP, RNAseq, e.g., \Biocpkg{edgeR}, \Biocpkg{goseq}
  \item Annotation -- gene or coordinate centric
  \item (Variants)
  \end{itemize}
\end{frame}

\begin{frame}{Five exercises}
  \begin{enumerate}
  \item Sequence I/O \& manipulation
  \item Coordinate-based annotation \& counting hits
  \item Operations on ranges
  \item Coverage and rle's.
  \item Whole-genome sequences
  \end{enumerate}
\end{frame}

\begin{frame}{\Bioconductor{}}
  Who
  \begin{itemize}
  \item FHCRC: Herv\'e Pag\`es, Marc Carlson, Nishant Gopalakrishnan,
    Valerie Obenchain, Dan Tenenbaum, Chao-Jen Wong
  \item Robert Gentleman (Genentech), Vince Carey (Harvard / Brigham
    \& Women's), Rafael Irizzary (Johns Hopkins), Wolfgang Huber (EBI,
    Hiedelberg)
  \item A large number of contributors, world-wide
  \end{itemize}
  Resources
  \begin{itemize}
  \item \href{http://bioconductor.org}{http://bioconductor.org}:
    installation, packages, work flows, courses, events
  \item Mailing list: friendly prompt help
  \item Conference: Morning talks, afternoon workshops, evening
    social. 28-29 July, Seattle, WA. Developer Day July 27
  \end{itemize}
\end{frame}


\end{document}