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

Abstract

Abstract 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 ( https://github.com/vaquerizaslab/fanc ). 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

• Chromosome conformation capture
• Hi-C
• Hi-C analysis
• Topologically associating domains (TAD)
• Chromosomal compartments
• Chromatin loops