Command Line Tool

PyGNA provides a complete analysis pipeline from command line.

The user can easily have summary statistics on a network or a single dataset or run a full analysis complete with visualisation features. Here we describe how to access all of them.

• Network Info
  • Network Properties
  • Cytoscape visualisation
  • Connected components
• Large Matrices creation
  • Shortest Paths matrix
  • Diffusion matrix
• Converting tables and names
  • Dataset from table
  • Convert gene names
• Geneset Network Topology Analysis
  • GNT Module analysis
  • GNT Degree analysis
  • GNT Shortest Path Analysis
  • GNT Random Walk Analysis
• Geneset Network Association Analysis
  • GNA Shortest Path
  • GNA Random Walk
• Weights Diffusion Analysis
  • Test diffusion hotnet
• Hypothesis testing
  • Degree corrected sampling
  • GNA: association sampling
• Visualisation
  • GNT plots
  • GNA plots