Thesis.tex

%!TEX root = Thesis.tex
%% ----------------------------------------------------------------
%% Author: Franceso Georg Schmitt
%%         s8foschm@stud.uni-saarland.de
%% ---------------------------------------------------------------- 

% Set up the document
\documentclass[a4paper, 11pt, twoside]{Thesis}  % Use the "Thesis" style defined in Thesis.cls
\graphicspath{{./Figures/}}  % Location of the graphics files (set up for graphics to be in PDF format)
\setchapterpath{./Chapters/}
\setappendixpath{./Appendices/}

% Include any extra LaTeX packages required
\usepackage[square, numbers, comma, sort&compress]{natbib}  % Use the "Natbib" style for the references in the Bibliography
\usepackage{verbatim}  % Needed for the "comment" environment to make LaTeX comments
\usepackage{verbatimbox}
\usepackage[usenames]{xcolor}
\usepackage{tabularx}
\usepackage{diagbox}
\usepackage{multirow}
\usepackage{wrapfig}
\usepackage{framed}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{stmaryrd}
\usepackage{framed}
\usepackage{hyperref}
\usepackage{todonotes}
\reversemarginpar
\presetkeys{todonotes}{noinline, line, tickmarkheight=0.1cm, color=orange!40, size=\tiny, prepend}{}
\usepackage{listings}
\lstset{language=C,numbers=left}
\usepackage{longtable}
\usepackage{multicol}
\usepackage{xifthen}
\usepackage{float}
\usepackage[nodayofweek]{datetime}


%% Specify thesis parameters here
%% ----------------------------------------------------------------
\setboolean  {proposal}{false} % disables all stuff that is not needed for a proposal if set to true
\university  {Saarland University}{http://www.uni-saarland.de/}
\department  {Department of Computer Science}{http://www.cs.uni-saarland.de/}
\group       {Center for Bioinformatics}{https://zbi-www.bioinf.uni-sb.de/en/index.html}
\faculty     {Faculty of Mathematics and Computer Science}{https://www.uni-saarland.de/fakultaet/mi.html}
\supervisor  {Prof. Dr. Hans-Peter Lenhof}
\advisor     {Kerstin Lenhof, Dr. rer. nat.}
\secondadvisor {Lea Eckhart, M. Sc.}
\examiner    {Prof. Dr. Hans-Peter Lenhof}
\secondexaminer {Prof. Dr. Volkhard Helms}
\degree      {Bachelor Of Science}
\thesiskind  {Bachelor's Thesis}
\authors     {Francesco Georg Schmitt}
%\thesistitle {Gene Set Enrichment Analysis on GDSC Datasets using GeneTrail}
\thesistitle {Enrichment Analyses for the Identification of Drug Response Markers in Cancer Cell Lines}
\newdate{date}{25}{11}{2024}
\date        {\displaydate{date}}
%\subject     {}
%\keywords    {}
%% ----------------------------------------------------------------

% If this is a proposal prepend 'Proposal for a' to thesiskind
\doifproposal{
	\let\thesisnameproposal\thesisname
	\thesiskind{Proposal for a \thesisnameproposal}
}

% Enable git revision parsing (Note: you need to enable shell-excape and pipe support for this feature to work)
%\revision{\input{|"git rev-parse HEAD | cut -c 1-8"}}

\begin{document}
\sloppy
\frontmatter	  % Begin Roman style (i, ii, iii, iv...) page numbering

%% Title Page
%% ----------------------------------------------------------------
\maketitle

%% Declaration Page required for the Thesis, your institution may give you a different text to place here
%% ----------------------------------------------------------------
\doifnotproposal{
\begin{declaration}
  \begin{center}
    \bf \large
    Eidesstattliche Erkl\"{a}rung
  \end{center}
  Ich erkl\"{a}re hiermit an Eides Statt,
  dass ich die vorliegende Arbeit selbstst\"{a}ndig verfasst und keine
  anderen als die angegebenen Quellen und Hilfsmittel verwendet habe. Das KI-Tool ChatGPT von OpenAI wurde zu Recherchezwecken und als Formulierungshilfe verwendet. Der gesamte Inhalt wurde jedoch eigenst\"{a}ndig vom Autor verfasst.

  \begin{center}
    \bf \large
    Statement in Lieu of an Oath
  \end{center}
  I hereby confirm that I have written this thesis on my own and 
  that I have not used any other media or materials than the ones
  referred to in this thesis. The AI tool ChatGPT by OpenAI was used for research purposes and to aid in the formulation of certain sections. However, all contents were independently written by the author.

  \vfill
  \begin{center}
    \bf \large
    Einverst\"{a}ndniserkl\"{a}rung
  \end{center}
  Ich bin damit einverstanden, dass meine (bestandene) Arbeit in beiden 
  Versionen in die Bibliothek der Informatik aufgenommen und damit 
  ver\"{o}ffentlicht wird. 

  \begin{center}
    \bf \large
    Declaration of Consent
  \end{center}
  I agree to make both versions of my thesis (with a passing grade) 
  accessible to the public by having them added to the library of the
  Computer Science Department.

  \vfill
  \vfill
  
  Ort, Datum/Place, Date:\hspace{1cm} Saarbrücken, 25.11.2024\\
  \rule[1em]{25em}{0.5pt}  % This prints a line to write the date

  Unterschrift/Signature:\\
  \rule[1em]{25em}{0.5pt}  % This prints a line for the signature
   
\end{declaration}
  \cleardoublepage  % Declaration ended, now start a new page
}

%% The Abstract Page
%% ----------------------------------------------------------------
\begin{abstract}
	\input{\chapterpath Abstract}
\end{abstract}

\doifnotproposal{

%% The Acknowledgements page, for thanking everyone
%% ----------------------------------------------------------------
\begin{acknowledgements}

First of all, I would like to thank my supervisor Prof.\ Dr.\ Hans-Peter Lenhof for providing me the opportunity to write my Bachelor's thesis at his chair. I would also like to thank Prof.\ Dr.\ Volkhard Helms for reviewing my thesis.

I owe my most sincere gratitude to my advisors, Lea Eckhart and Kerstin Lenhof. They were always open for questions and supported me immensely in the process of working on this thesis, and most importantly, always kept their patience, even when the whole process ended up taking much longer than it should have. They also always provided extensive and constructive feedback during the writing of this thesis.

For proofreading, I would like to thank my dear friends Mara Klee, Tobias Wiedemann, Alex Umansky and, especially, my sister Angelina Schmitt.

Finally, I want to thank my family for keeping the positive pressure on when my motivation was at a low, as well as their unwavering support throughout my studies, which I immensely appreciate.

\end{acknowledgements}
\cleardoublepage
}

%% Table of Contents
%% ----------------------------------------------------------------

\tableofcontents
\clearpage

%% The Dedication page
%% ----------------------------------------------------------------
%\doifnotproposal{
%  \thispagestyle{empty}  % Page style needs to be empty for this page
%  \dedicatory{Dedicated to WHATEVER.}
%}

\mainmatter	  % Begin normal, numeric (1,2,3...) page numbering

%% Chapters
%% ----------------------------------------------------------------
% Include the chapters of the thesis, as separate files (careful of case-sensitivity and spaces in filenames)
% Capitalized chaptertitles generally look better

\loadchapter{Intro}{Introduction}{Introduction}
\loadchapter{Bio}{Biology of Cancer \\ and Model Systems}{Biology of Cancer and Model Systems}
\loadchapter{Math}{Mathematical Methods}{Mathematical Methods}
\loadchapter{Mats}{Materials}{Materials}
\loadchapter{Impl}{Study Design and Implementation}{Study Design and Implementation}
\loadchapter{Results}{Results}{Results}
\loadchapter{Discussion}{Discussion}{Discussion}


\clearpage

%% Appendices
%% ----------------------------------------------------------------
\appendix

%\input{./Appendices/AppendixA}	% Appendix Title

%\input{./Appendices/AppendixB} % Appendix Title

%\input{./Appendices/AppendixC} % Appendix Title


\backmatter

%% Lists of figures and tables
%% ----------------------------------------------------------------
\doifnotproposal{
	\lhead{\emph{List of Figures}}
	\addtotoc{List of Figures}
	\listoffigures
	\clearpage

  	\addtotoc{List of Tables}
  	\lhead{\emph{List of Tables}}
	\listoftables
	\clearpage
}

%% Bibliography
%% ----------------------------------------------------------------
\label{Bibliography}
\addtotoc{Bibliography}
\lhead{\emph{Bibliography}}  % Change the left side page header to "Bibliography"
\bibliographystyle{unsrtnat}  % Use the "unsrtnat" BibTeX style for formatting the Bibliography
\bibliography{Bibliography}  % The references (bibliography) information are stored in the file named "Bibliography.bib"

\appendix%Begins the appendix
\lhead{\emph{Appendix}}
\renewcommand{\chaptername}{Appendix} % Ensure chapters are labeled "Appendix"
\renewcommand{\thechapter}{\Alph{chapter}} % Use letters (A, B, ...) for chapter numbering
%\setcounter{chapter}{1}
%\loadappendix{Across-drug Analysis of Enrichment and Depletion Count}{bidirectional-bar-plots}
\stepcounter{chapter}
\chapter{Across-drug Analysis of Enrichment and Depletion Count}\label{appendix:bidir}
\input{Appendices/bidirectional-bar-plots}
%\loadappendix{Principal Component Analysis}{pca-plots}
\stepcounter{chapter}
%\setcounter{section}{0} % Reset section numbering for the new appendix
\chapter{Principal Component Analysis}\label{appendix:pca}
\input{Appendices/pca-plots}
\end{document}  % The End