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v2020

Contents:

  • Data Collection
    • TCGA
    • PCAWG
    • cBioPortal
    • Hartwig Medical Foundation
    • ICGC
    • St. Jude
    • PedcBioPortal
    • TARGET
    • Beat AML
    • Literature
  • Preprocessing
  • Methods for cancer driver gene identification
    • dNdScv
    • OncodriveFML
    • OncodriveCLUSTL
    • cBaSE
    • Mutpanning
    • HotMaps3D
    • smRegions
  • Combining the outputs of driver identification methods
    • Rationale
    • Weight Estimation by Voting
    • Ranking Score
    • Optimization with constraints
    • Estimation of combined p-values using weighted Stouffer Z-score
    • Tiers of driver genes from sorted list of combined rankings and p-values
    • Combination benchmark
      • Datasets for evaluation
      • Metrics for evaluation
      • Comparison with individual methods
      • Leave-one-out combination
      • Comparison with other combinatorial selection methods
  • Drivers postprocessing
    • Classification according to annotation level from CGC
    • Mode of action of driver genes
  • Repository of mutational features
    • Linear clusters
    • 3D clusters
    • Pfam Domains
    • Excess of mutations
    • Mode of action
  • Installation
  • Usage
  • Input & output
    • Input
    • Output
IntOGen
  • Docs »
  • Index
  • Edit on Bitbucket

Index

Symbols

Symbols

  • --annotations <file>
  • --containers <path>
  • --datasets <path>
  • --debug true
  • --input <path>
  • --output <path>
  • -resume

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