mphil-thesis

Source for the PDF is in the LaTeX directory. Full text of the thesis is in Edridge DSouza MPhil Thesis.pdf. Click this link to view the PDF in browser.

Within the Computation directory, each subdirectory represents a different portion of the project. All files are provided except for the files in the data directories, as well as any .RDS data files. However, following the 00_setup.sh script in any of the project directories will create the data directory necessary to run the scripts.

• 2019_11_04_scRNAseq analysis contains the embryonic dataset from Karaiskos et al. (referred to as zinzen in the code).

• 2020_04_01_Avalos_scRNA contains the larval brain dataset from Avalos et al. (referred to as avalos).

• 2020_04_29_Allen_VentralNerveCord contains the adult VNC dataset from Allen et al. (referred to as allen).

• 2020_04_29_ClusterMap contains the ClusterMap attempt on the local Ubuntu machine (the remainder can be found in Rustbucket Analyses).

• 2020_07_03_PutItTogether contains an exhaustive set of Gene Ontology plots for all the SoxB-positive clusters in each of the datasets. The ___.markers.csv files also provide a full list of markers for each cluster.

• Cytoscape contains figures as well as the network file for the Cytoscape analysis.

• Rustbucket Analyses contains the "regular" and "by the book" analyses for the adult VNC dataset, which was performed on the Rustbucket server. It also contains the other half of the ClusterMap attempted analysis. "By the book" was the version ultimately used for the adult VNC analysis in the text.

Post-defense revisions have also been added.