HiC-Bench_manual.tex

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\title{HiC-Bench Manual}
\author{Stephen M. Kelly\,$^{1,}$$^{2}$, Charalampos Lazaris\,$^{3,}$$^{4,}$$^{5}$, Aristotelis Tsirigos\,$^{1,}$$^{2,}$$^{3,}$$^{4,}$$^{5}$
\\
\footnotesize $^{1}$ Applied Bioinformatics Center, Office of Collaborative Science, NYU School of Medicine, NY 10016, USA\\
\footnotesize $^{2}$ Genome Technology Center, Office of Collaborative Science, NYU School of Medicine, NY 10016, USA\\
\footnotesize $^{3}$ Department of Pathology, NYU School of Medicine, New York, New York 10016, USA\\
\footnotesize $^{4}$ NYU Cancer Institute and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA\\
\footnotesize $^{5}$ Center for Health Informatics \& Bioinformatics, NYU School of Medicine, NY 10016, USA\\
}

\date{\today}

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{\footnotesize \tableofcontents \listoffigures}

\section{Introduction} % basic description of the pipeline and its usage
\input{child/Introduction/install-setup-run.tex}
\input{child/Introduction/dependencies.tex}
\clearpage

\section{Default Pipeline Components} \label{default-pipeline} % description of pipeline components
\input{child/default-pipeline-components.tex}
\clearpage

% come back to this section
% \section{Pipeline Code Structure} \label{code-structure}
% \input{child/code-structure.tex}
% \clearpage

% hold off on auto report
% \section{Automatic Reports} \label{auto-report} % description of automatic reports and their components
% \input{child/auto_report.tex}
% \clearpage

% move this to the intro
% \section{Dependencies} \label{dependency}% description of dependencies needed
% \clearpage

% hold off on this section as well
% \section{Modifying the Pipeline} \label{custom-pipeline-step} % requirements for modifying the pipeline
% \input{child/custom_pipeline_step.tex}
% \clearpage
\section[Custom Pipeline Steps]{Adding Custom Pipeline Steps}\label{custom-pipeline-steps}%
\input{child/Appendix/custom-pipeline-step.tex}


\section{HiC-Seq Pipeline}
\input{child/HiC/index.tex}
\input{child/HiC/align.tex}% __01a-align
\input{child/HiC/filter.tex} % __02a-filter
\input{child/HiC/filter-stats.tex}% __02b-filter-stats
\input{child/HiC/tracks.tex}% __03a-tracks
\input{child/HiC/matrix-filtered.tex}% __04a-matrix-filtered
\input{child/HiC/matrix-prep.tex}% __05a-matrix-prep
\input{child/HiC/matrix-ic.tex}% __06a-matrix-ic
\input{child/HiC/matrix-hicnorm.tex}% __07a-matrix-hicnorm
\input{child/HiC/matrix-stats.tex}% __08a-matrix-stats
\input{child/HiC/compare-matrices.tex}% __09a-compare-matrices
\input{child/HiC/compare-matrices-stats.tex}% __09b-compare-matrices-stats
\input{child/HiC/boundary-scores.tex}% __10a-boundary-scores
\input{child/HiC/boundary-scores-pca.tex}% __10b-boundary-scores-pca
\input{child/HiC/domains.tex}% __11a-domains
\input{child/HiC/compare-boundaries.tex}% __12a-compare-boundaries
\input{child/HiC/compare-boundaries-stats.tex}% __12b-compare-boundaries-stats
\input{child/HiC/hicplotter.tex}% __13a-hicplotter
\input{child/HiC/interactions.tex}% __14a-interactions
\input{child/HiC/annotations.tex}% __15a-annotations
\input{child/HiC/annotations-stats.tex}% __15b-annotations-stats
% \clearpage

\section{Appendix}
\input{child/Appendix/appendix.tex}
\input{child/Appendix/gtools-hic.tex}
\input{child/Appendix/pipeline-master-explorer.tex}

% \input{child/Appendix/gtools-overlaps.tex} % don't include this one

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\subsection{System and Session Information}\label{session}
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## R version 3.2.3 (2015-12-10)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS release 6.7 (Final)
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