Alternative splicing programs in tumor development and progression

This repository includes all the resources necessary to recreate the results of the thesis titled "Alternative splicing programs in tumor development and progression" submitted to the McGill University in partial fulfillment of the requirements of the degree of Master of Science in Human Genetics in December 2023.

Data availability

The datasets pertaining this work have been deposited in several Zenodo collections that follow the same structure of the thesis:

Chapter 2 - Materials and Methods

• 2.1 TRex method
  • Part 1 - simulated data
  • Part 2 - TCGA data
• 2.2 Benchmarking TRex using simulated RNA-seq datasets
• 2.3 TCGA analysis
• 2.4 Functional analysis of alternative splicing events of interest
• 2.5 Analysis of alternative splicing regulators

Chapter3 - Results

All the input objects required to reproduce the notebooks can be downloaded from

The notebooks found under Chapter3_Results are organized in the following manner:

• 3.1 Study overview
  Figure 5, Supplementary data table 1

• 3.2 Tumour purity has a strong cancer-specific effect on the quantification of alternative splicing
  Figure 6, Supplementary figures S1, S2 and S3

• 3.3 TRex outperforms state-of-the-art and removes confounders of differential alternative splicing
  Figure 7, Supplementary figure S4

• 3.4 A pan-cancer map of unbiased alternative splicing programs reveals context-dependant and global patterns of dysregulation in cancer
  Figure 8, Supplementary figures S5-S14

• 3.5 TRex detects neoplastic splicing programs in a case study of clear-cell Renal Cell Carcinoma
  Figure 9, Supplementary figures S15 and S16

• 3.6 RNA binding proteins as regulators of splicing programs associated with tumour development
  Figure 10, Supplementary figures S16-S20

Supplementary data tables

Suppementary Data Tables 1-2