Analyse Hi-C matrices (API)

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