We studied the functional impact of alternative splicing alterations in cancer, with special interest on their potential as tumor drivers. The article is available in Cell Reports.

Analyses

Manuscript figures and tables

• Manuscript figures
• Manuscript supplementary figures
• Manuscript supplementary files

Switches

• Switch statistics
• Immune cells/stroma contamination
• Functionality
• Tumorigenic evidences
• Events involved
• PSI study

Mutations

• Whole-exome sequencing gene analysis
• Whole-genome sequencing gene analysis
• CNA analysis
• Mutual exclusion: comet

Structure

• Pfam domains
• Protein-protein interactions
• Protein-protein interactions stats
• Protein-protein interactions mutual exclusion
• Protein-protein interactions neighborhoods
• Neighborhood curation

Data

The data was generated by applying the spada and scudo pipelines to transcript expression data generated by the TCGA project. The files necessary to replicate all these analyses are available here; it must be placed in a data/ folder inside the project.

Dependencies

This Jupyter notebook requires the following external libraries to function:

• find.me
• ggstars
• tidyverse
• magrittr
• UpSetR
• cowplot
• network
• ggnetwork
• igraph
• intergraph