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external link: developed by Kai Kruse and Clemens B. Hug in the Vaquerizas Lab (


FAN-C is 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. It is natively compatibile with the most prevalent Hi-C storage formats, including Juicer and Cooler files, and therefore can be used in combination with a large number of existing analysis tools, thus greatly simplifying Hi-C matrix analysis.

A small selection of features: Automated Hi-C matrix generation pipeline from raw reads to filtered and balanced Hi-C matrix; expected values and O/E matrices; AB compartment, correlation and eigenvector analysis; insulation score and directionality index calculation, boundary calls; matrix and region comparisons; aggregate and saddle analyses, CPU-based loop calling using the HICCUPS algorithm; interconversion of different Hi-C file formats, including Cooler, Juicer, HiC-Pro, 4DNucleome pairs, ...; interactive visualisation and highly customisable plotting API for creating publication-ready figures

How to cite

Kruse K, Hug CB, & Vaquerizas JM. FAN-C: A Feature-rich Framework for the Analysis and Visualisation of C data. bioRxiv, doi: