pymaftools

Python package for handling and analyzing Mutation Annotation Format (MAF) files.

User Guide

• Getting Started
  • Installation
  • Quick Start
  • Saving Results
  • Reading MAF Files
  • Computing TMB
  • Subsetting Data
  • Multi-omics Integration
• PivotTable
  • From a MAF
  • Inspecting the structure
  • Persistence
  • Subsetting
  • Mutation frequency
  • Sorting
  • Multi-omics integration
• OncoPlot
  • Start simple
  • Add metadata strips
  • Group rows and columns
  • Putting it together: a real cohort

API Reference

• Core Modules
  • MAF
  • VCF
  • PivotTable
  • Cohort
  • CopyNumberVariationTable
  • ExpressionTable
  • SignatureTable
  • CancerCellFractionTable
  • PairwiseMatrix
  • Clustering
• Plot Modules
  • OncoPlot
  • Track
  • LollipopPlot
  • PivotStatsPlot
  • ExpressionTablePlot
  • CopyNumberVariationTablePlot
  • SignatureTablePlot
  • SmallVariationTablePlot
  • ModelPlot
  • MethodsPlot
  • BasePlot
  • ColorManager
  • FontManager
  • LegendManager
• Model Modules
  • StackingModel
  • modelUtils
• I/O Modules
  • TCGA Builders
  • VCF Parsing
• Utility Modules
  • geneset
  • reduction
  • geneinfo

Indices and tables

• Index

• Module Index