footprints/report/Supplementary.Rnw at master · saezlab/footprints · GitHub

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\documentclass{article}
\usepackage[margin=1in]{geometry}

\input{config}

%\title{Supplementary Material for "Perturbation-response genes reveal signaling
%    footprints in cancer gene expression"}
%\author{Michael Schubert
%    \and Bertram Klinger
%    \and Martina Kl{\"u}nemann
%    \and Anja Sieber
%    \and Florian Uhlitz
%    \and Sascha Sauer
%    \and Mathew J Garnett
%    \and Nils Bl{\"u}thgen
%    \and Julio Saez-Rodriguez}

\begin{document}

%\maketitle
%\tableofcontents
%\newpage

\section*{Supplementary notes}

\Sexpr{knit_child('note_searchterms.Rnw')} %TODO: re-enable (lots of HTTP queries)

%\subsection{R packages used}
%
%<<session_info>>=
%sessionInfo()
%@

\section*{Supplementary tables}

%\begin{table}[H]
%\centering
%\caption{Coefficients matrix of the fitted PROGENy model, provided as a
%    separate file. HGNC gene names in rows, pathways in columns.}
%\end{table}

\captionsetup[subfloat]{position=top}

\Sexpr{knit_child('roc_auc.Rnw')}

\Sexpr{knit_child('pathway_mapping.Rnw')}

\Sexpr{knit_child('mut_cna_table.Rnw')}

\Sexpr{knit_child('drug_over_mut_stats.Rnw')}

\Sexpr{knit_child('drug_ccle.Rnw')}

\Sexpr{knit_child('survival_bootstrap.Rnw')}

%\begin{table}[H]
%\centering
%\caption{log2 fold changes of phosphoproteomic measurements over BSA,
%    provided as a separate file.}
%\end{table}

\section*{Supplementary figures}

\captionsetup[subfloat]{position=bottom}

\Sexpr{knit_child('dataset_overview.Rnw')}

\Sexpr{knit_child('model_significance.Rnw')}

\Sexpr{knit_child('signature_overlap.Rnw')}

\Sexpr{knit_child('signature_go.Rnw')}

\Sexpr{knit_child('perturb_compare.Rnw')}

\Sexpr{knit_child('roc.Rnw')}

\Sexpr{knit_child('signature_validation.Rnw')}

\Sexpr{knit_child('basal_correlation.Rnw')}

\Sexpr{knit_child('mut_volcanos.Rnw')}

%\Sexpr{knit_child('cna_volcanos.Rnw')}

\Sexpr{knit_child('drug_volcanos.Rnw')}

\Sexpr{knit_child('survival_tissue_volcanos.Rnw')}

\printbibliography[heading=bibintoc,title={Supplementary References}]

\end{document}