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\title{Introduction}
\author{Martin T.\ Morgan\footnote{\url{mtmorgan@fhcrc.org}}}
\date{27-28 February 2014}

\begin{document}

\maketitle

\begin{frame}{Introduction: \Bioconductor}
  Analysis and comprehension of high-throughput genomic data
  \begin{itemize}
  \item \url{http://bioconductor.org}
  \item $>11$ years old, $749$ packages
  \end{itemize}
  Themes
  \begin{itemize}
  \item Rigorous statistics
  \item Reproducible work flows
  \item Integrative analysis
  \end{itemize}
\end{frame}

\begin{frame}{Introduction: \Bioconductor}
  \begin{columns}
    \column{.5\textwidth}
    \begin{itemize}
    \item 1341 PubMed full-text citations in trailing 12 months
    \item 28,000 web visits / month; 75,000 unique IP downloads / year
    \item Annual conferences; courses; active mailing list; \ldots
    \end{itemize}
    \column{.5\textwidth}
    \includegraphics[width=\textwidth]{figures/usage-geography}
  \end{columns}
  \bigskip\par
  \textbf{\Bioconductor{} Conference}, July 30 - Aug 1, Boston, USA
\end{frame}

\begin{frame}{Introduction: What is \Bioconductor{} good for?}
  \begin{itemize}
  \item Microarrays: expression, copy number, SNPs, methylation, \ldots
  \item Sequencing: RNA-seq, ChIP-seq, called variants, \ldots 
    \begin{itemize}
    \item Especially \emph{after} assembly / alignment
    \end{itemize}
  \item Annotation: genes, pathways, gene models (exons, transcripts,
    etc.), \ldots
  \item Flow cytometry, proteomics, image analysis, high-throughput
    screens, \ldots
  \end{itemize}
\end{frame}

\begin{frame}{Acknowledgements}
  \begin{itemize}
  \item \Bioconductor{} team: Sonali Arora, Marc Carlson, Nate Hayden,
    Valerie Obenchain, Herv\'e Pag\`es, Paul Shannon, Dan Tenenbaum
  \item Technical advisory council: Vincent Carey, Wolfgang Huber,
    Robert Gentleman, Rafael Irizzary, Sean Davis, Kasper Hansen
  \item Scientific advisory board: Simon Tavar\'e, Vivian Bonazzi,
    Vincent Carey, Wolfgang Huber, Robert Gentleman, Rafael Irizzary,
    Paul Flicek, Simon Urbanek.
  \item NIH / NHGRI U41HG0004059
  \item The \Bioconductor{} community
  \end{itemize}
\end{frame}

\begin{frame}
  Introductions
\end{frame}

\end{document}
