fanc Python module

• Quickstart
  • Loading datasets
  • Logging
• Working with Juicer and Cooler files
  • Cooler .cool and .mcool
  • Juicer .hic files
• Interfaces
  • Genomic regions (RegionBased interface)
  • Edges (contacts, pixels, ...) (RegionPairsContainer interface)
  • Matrices (RegionMatrixContainer interface)
• Generate Hi-C matrices (API)
  • Mapping FASTQ files
  • Generating and filtering ReadPairs
  • Generating, binning, and filtering Hic objects
• Analyse Hi-C matrices (API)
  • Expected values and O/E matrices
  • AB compartments
  • PCA analysis
  • TADs and TAD boundaries
  • Matrix and score comparisons
  • Aggregate analysis
  • Loop calling
• Plotting (API)
  • Plotting basics
  • Matrix plots
  • Region and score plots
• Reference
  • init
  • map
  • regions
  • pairs
  • matrix
  • hic
  • peaks
  • compatibility
  • architecture
  • plotting
  • tools