FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data

Genome Biol. 2020 Dec 17;21(1):303. doi: 10.1186/s13059-020-02215-9.


Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we present FAN-C, an easy-to-use command-line tool and powerful Python API with a broad feature set covering matrix generation, analysis, and visualisation for C-like data ( ). Due to its compatibility with the most prevalent Hi-C storage formats, FAN-C can be used in combination with a large number of existing analysis tools, thus greatly simplifying Hi-C matrix analysis.

Keywords: Chromatin loops; Chromosomal compartments; Chromosome conformation capture; Hi-C; Hi-C analysis; Hi-C visualisation; Topologically associating domains (TAD).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin
  • Chromosomes / chemistry*
  • Computational Biology
  • Embryonic Stem Cells
  • Genomics
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Molecular Conformation*


  • Chromatin