rebuttal.tex

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\title{Rebuttal: response to doctoral committee comments}
\author{Louise Deconinck}
\date{}

\maketitle

I would like to start by offering my sincere gratitude for the insightful comments made by all committee members.

I have addressed a number of the comments and recommendations made by the committee members. The following part of this document lists them, and the accompanying file details all the changes made to the manuscript.

\section{Various small mistakes and clarifications.}
Throughout the manuscript, various spelling and grammatical mistakes have been corrected. Small clarifications have been made whenever requested. See the accompanying file for all changes made to the manuscript.

\section{Structure}
In accordance with feedback from the committee members received in the reading reports, as well as during the closed defense, the structure of the dissertation has been updated to more closely reflect the different parts. The dissertation now consists of five parts: Trajectory inference, Interoperability, Visualization, Reflections and Appendices, with an introductory chapter at the start of the document.

\section{Changes made to chapter: Introduction}
\begin{itemize}
\item A subsection on data characteristics, discussing dropout and imputation and metacell techniques was added.
\item A clarification was made to explain why finding similarities in single-cell data is necessary.
\item The section on highly variable gene selection was clarified.
\item Information on three batch effect correction methods, scGen, fastMNN, and Scanorama, was provided.
\item A section on graph-based algorithms useful in trajectory analysis was added, discussing Maximum Spanning Trees, Dynamic Time Warping and Bipartite graph matching.
\item More information was provided on the aims of this dissertation with regard to trajectory inference. Parts of the reflections were moved to the introduction.
\item A small paragraph on spatial trajectory inference methods was added.
\item The research context and objectives of this thesis were clarified and link back to the challenges posed in the earlier section.

\end{itemize}

\section{Changes made to chapter: Recent advances in trajectory inference from single-cell omics data}
Mistakenly, the non-peer reviewed text for this chapter was included in the earlier version of this dissertation. This has been rectified, and the dissertation now contains the peer-reviewed published text.

\section{Changes made to chapter: dynchro: exploratory analysis and alignment of inferred trajectories}

\begin{itemize}
\item This chapter was renamed to be more descriptive of the contents.
\item Links to the dynchro repository and the use cases described in the chapter have been included.
\end{itemize}

\section{Changes made to chapter: Polyglot programming for single-cell analysis}
\begin{itemize}
\item This chapter was renamed to more closely resemble the content.
\item Colloquial language was removed.
\item Code necessary for the workflow framework use case has been moved to an appendix to increase legibility of the chapter.
\item A conclusion/guidelines section was added.
\end{itemize}

\section{Changes made to Perspectives}
\begin{itemize}
\item A part of the section on trajectory inference methods has been moved to the introduction.
\item A paragraph on the difficulty of obtaining ground truth information has been added.
\end{itemize}

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