Code relating to analysis of alternative splicing events - ICGC / PCAWG-3

This public repository contains the research and analysis code that was used to generate the results presented in the publication "Genomic basis for RNA alterations in cancer."

The code is organized across several directoris:

• event_calling The scripts used to call the alternative splicing events from aligned RNA-Seq data
• exonizations Code related to detecting exonization events from the splicing graph data
• filter_events Code filtering for potentially functional events (used for gene centric analysis)
• gene_centric_tables Code summarizing the alternative splicing events of all samples into a splice-outlier table
• icgc_anno, icgc_colors, icgc_utils Helper and utility code to take care of logistics and metadata
• junction_db Scripts to collect all aligned splice junctions into a joint database
• pca_tsne Scripts using dimensionality reduction for visualization
• stats_events Code summarizing the event statistics
• utils Utility and helper functions