FAN-C documentation

• Getting started with FAN-C
  • Overview
  • Installation
    • Prerequisite: HDF5
  • Building this documentation
  • Example analysis
    • Plotting
    • Next steps
• fanc: command line tools
  • Overview and shared parameters
    • Overview
    • Logging
    • Email notifications
    • Temporary files
    • FAN-C config files
    • NumExpr ThreadPool configuration
  • Working with Cooler, Juicer, and text files
    • Cooler .cool and .mcool
    • Juicer .hic files
    • Text files
  • Generate Hi-C matrices
    • fanc auto: Automated generation of Hi-C matrices
    • Individual pipeline steps
    • Helper tools
    • Configuration options
  • Analyse Hi-C matrices
    • Expected values and O/E matrices
    • AB compartments
    • PCA
    • TADs and TAD boundaries
    • Matrix and score comparisons
    • Aggregate Hi-C matrices
    • Loop calling
• fancplot: plotting from the command line
  • Overview and basic usage
    • Overview
    • Setting up the figure and plotting regions
    • Adding panels
    • Common parameters
  • Working with Cooler, Juicer, and text files
    • Cooler .cool and .mcool
    • Juicer .hic files
    • Text files
  • Panel types
    • Matrix panels
    • Region and score panels
• Python API
  • 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

Indices and tables

• Index
• Module Index
• Search Page