This repository stores the code written by Antonio Ortega during his Master Thesis in Bioinformatics at the University of Copenhagen in Denmark (Københavns Universitet). The code is split in 2 folders:
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pipeline: bash, R and Python scripts required to run an OS label-free proteomics quantification pipeline in Linux using the tools published by the Compomics group at University of Ghent. -
model: Python scripts powering BayesQuant, a program that uses probabilistic programming to compute relative quantities from MS1 intensity data, in a format similar to that used by MSqRob. It consists of a PyMC3 model.
Additionally, the thp1 folder stores data in different processing stages analysed by the pipeline for a benchmark dataset of THP1 cells.
Another repo contains the latex code required to compile the PDF document, available here .