Master Thesis Bioinformatics

This is the repo with all the source material for my bioinformatics master thesis "Cancer Transcriptome Cleaning by Deconvolution".

You can find the submitted thesis PDF in the Final Thesis release.

Building the Document

Quick start

If Guix is installed, building the document via the quick_start.sh script is easy:

bash quick_start.sh

Otherwise, you need to ensure the packages defined in manifest.scm are installed prior to running the quick start script.

Manual Build

First, the archived run summary resources need to be unpacked:

tar -xzf "run_summary_archive.tar.gz"

Then, the the thesis document can be rendered using the render_book.R script:

Rscript --vanilla render_book.R

That will output both an PDF and HTML version into the project dir.