Oncodrive3D Analysis

This repository includes notebooks to reproduce the analysis performed for the publication of Oncodrive3D.

Notebooks

0. genetables
   • Data preprocessing
1. method_explaination
   • Toy example to explain the method: F1
   • Scores and pvalues calculation: Supplementary Methods F1
2. enrichment
   • CGC and Fish genes enrichment analysis: F2, S2
3. detected_genes_and_complementarity
   • Number of detected genes: F2, S2, S11
   • Complementarity analysis: F4, S5, S6, S11, S12
4. resources_analysis
   • Resources utilization analysis: F3, S4
5. landscape_and_distributions
   • Landscape of cancer driver genes: F5, S8, S9
   • Tables: T1, T2, T3
   • Scores and features distributions: S7
   • Landscape of CH genes: S12
6. recurrence
   • Recurrence of clusters in cancer: F6
   • Recurrence of clusters in CH: S12
7. data
   • Data visualization: S1
8. qq_plots
   • QQ plots: S3