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HiC-Bench_manual.Rnw
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HiC-Bench_manual.Rnw
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\documentclass{article}
\usepackage[sc]{mathpazo} %
\renewcommand{\familydefault}{\sfdefault} % sets the default font type to sans-serif
\usepackage{helvet} % sets the font to Helvetica, scaled 95%
\usepackage[T1]{fontenc}
\usepackage{geometry}
\geometry{verbose,tmargin=2.5cm,bmargin=2.5cm,lmargin=2.5cm,rmargin=2.5cm}
\setcounter{secnumdepth}{3} % number for section levels, in text
\setcounter{tocdepth}{2} % inclusion of section levels in ToC
% %\usepackage{array,booktabs}
\usepackage{cite}
\usepackage[labelfont=bf]{caption}
\usepackage[unicode=true,pdfusetitle,
bookmarks=true,bookmarksnumbered=true,bookmarksopen=true,bookmarksopenlevel=2,
breaklinks=false,pdfborder={0 0 1},backref=false,colorlinks=trues]
{hyperref} % colorlinks=false
\definecolor{darkblue}{rgb}{0.0,0.0,0.3}
\hypersetup{colorlinks,breaklinks,
linkcolor=darkblue,urlcolor=darkblue,
anchorcolor=darkblue,citecolor=darkblue}
% %\hypersetup{pdfstartview={XYZ null null 1}} %this is knitr default
\usepackage{breakurl}
% \usepackage{etoolbox}
\usepackage{forloop}
\usepackage{tikz}
% \usepackage{subcaption}
\usepackage{amsmath}
\usepackage{graphicx}
\usepackage{url}
\usepackage{xcolor,colortbl}
% ~~~~~ for source code formatting
\usepackage{listings}
\usepackage{color}
\definecolor{mygreen}{rgb}{0,0.6,0}
\definecolor{mygray}{rgb}{0.5,0.5,0.5}
\definecolor{mymauve}{rgb}{0.58,0,0.82}
\lstset{ %
backgroundcolor=\color{white}, % choose the background color; you must add \usepackage{color} or \usepackage{xcolor}
basicstyle=\scriptsize, % the size of the fonts that are used for the code
breakatwhitespace=false, % sets if automatic breaks should only happen at whitespace
breaklines=true, % sets automatic line breaking
captionpos=b, % sets the caption-position to bottom
commentstyle=\color{mygreen}, % comment style
deletekeywords={...}, % if you want to delete keywords from the given language
escapeinside={\%*}{*)}, % if you want to add LaTeX within your code
extendedchars=true, % lets you use non-ASCII characters; for 8-bits encodings only, does not work with UTF-8
frame=single, % adds a frame around the code
keepspaces=true, % keeps spaces in text, useful for keeping indentation of code (possibly needs columns=flexible)
keywordstyle=\color{blue}, % keyword style
language=bash, % the language of the code
otherkeywords={*,...}, % if you want to add more keywords to the set
numbers=left, % where to put the line-numbers; possible values are (none, left, right)
numbersep=5pt, % how far the line-numbers are from the code
numberstyle=\tiny\color{mygray}, % the style that is used for the line-numbers
rulecolor=\color{black}, % if not set, the frame-color may be changed on line-breaks within not-black text (e.g. comments (green here))
showspaces=false, % show spaces everywhere adding particular underscores; it overrides 'showstringspaces'
showstringspaces=false, % underline spaces within strings only
showtabs=false, % show tabs within strings adding particular underscores
stepnumber=2, % the step between two line-numbers. If it's 1, each line will be numbered
stringstyle=\color{mymauve}, % string literal style
tabsize=2, % sets default tabsize to 2 spaces
title=\lstname % show the filename of files included with \lstinputlisting; also try caption instead of title
}
%%%%%%
% for the footer
% \usepackage{lastpage}
% \usepackage{fancyhdr}
% \pagestyle{fancy}
% \cfoot{\thepage\ of \pageref{LastPage}}
\usepackage{fancyhdr}% http://ctan.org/pkg/fancyhdr
\usepackage{lastpage}% http://ctan.org/pkg/lastpage
\pagestyle{fancy}% Set default page style to fancy
\renewcommand{\headrulewidth}{0pt}% Remove header rule
\fancyhead{}% Remove all header contents
\cfoot{Page \thepage\ of \pageref{LastPage}}% Page X of Y in the footer (centered)
%%%%%%%
% \usepackage{tabularx}
% \usepackage{tabulary}
\usepackage[absolute]{textpos} % use this for the header text block
%%%%%%
\listfiles % list the packages and versions used in the .log file upon compilation
%%%%
\begin{document}% there are some commands in latex you can mess with; never mess with this one
% Also, never mess with the following chunk unless you think you know what you're doing:
<<setup, include=FALSE, cache=FALSE>>=
# this is equivalent to \SweaveOpts{...}
opts_chunk$set(fig.path='figure/latex-', fig.align='center', fig.show='hold')
options(replace.assign=TRUE,width=90)
require(highlight)
@
\title{HiC-Bench Manual}
\author{Stephen M. Kelly\,$^{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}
\maketitle
% header block with logo
{\footnotesize
\textblockorigin{-18pt}{-2pt}
\begin{textblock*}{10cm}(2cm,1cm)
\includegraphics[height=2.5cm,keepaspectratio]{figure/NYULMC_white.jpg}
\end{textblock*}}
% old logo in center of page
% \begin{figure}[!h]
% \centering
% \includegraphics[height=2cm]{figure/NYULMC_white.jpg} % no image scaling
% % \caption{My caption}
% \label{fig:title-image}
% \end{figure}
{\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
% \newpage
% \pagebreak
\clearpage
\subsection{System and Session Information}\label{session}
This document was created with: \LaTeXe~ \fmtversion
<<Session>>=
system('uname -srv',intern=T)
sessionInfo()
@
\input{child/Appendix/file_list_latex.tex}
\end{document}