FAN-C
0.9.1
  • Getting started with FAN-C
  • fanc: command line tools
    • Overview and shared parameters
    • Working with Cooler, Juicer, and text files
    • Generate Hi-C matrices
    • 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
  • Python API
FAN-C
  • Docs »
  • FAN-C command line tools »
  • Analyse Hi-C matrices (API)
  • View page source

Analyse Hi-C matrices (API)ΒΆ

The fanc tool should be accessible from the command line after you installed FAN-C (see Installation). It provides convenient commands for the generation, modification, and analysis of Hi-C data.

Note

The following tutorials assume you have downloaded all the example data files from out GitHub page and ran the sample analysis outlined in Example analysis.

  • Expected values and O/E matrices
    • Positional Arguments
    • Named Arguments
    • Example
    • Options
    • Comparing expected values
    • O/E matrices
  • AB compartments
    • Positional Arguments
    • Named Arguments
    • Correlation matrix
    • AB Eigenvector
    • AB domains
    • AB enrichment profiles
  • PCA
    • Positional Arguments
    • Named Arguments
    • Example
    • Filters
  • TADs and TAD boundaries
    • Insulation Score
    • Insulating boundaries (TAD boundaries)
    • Directionality Index
    • A note on TAD calling
  • Matrix and score comparisons
    • Positional Arguments
    • Named Arguments
    • Compare matrices
    • Compare scores
    • Compare multi-score files
  • Aggregate Hi-C matrices
    • Positional Arguments
    • Named Arguments
    • Aggregate over variable size regions
    • Aggregate TADs
    • Fixed-width regions
    • Loops and other pairwise genomic regions
  • Loop calling
    • Positional Arguments
    • Named Arguments
    • Annotating pixels for loop calling
    • Filtering annotated pixels
    • Merging unfiltered pixels into loops
    • Exporting to BEDPE
Next Previous

© Copyright 2020, Kai Kruse, Vaquerizas lab

Built with Sphinx using a theme provided by Read the Docs.