FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
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FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data Kai Kruse1, Clemens B. Hug1 and Juan M. Vaquerizas1,2* * Correspondence: j.vaquerizas@lms. mrc.ac.uk; [email protected]. de 1 Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany 2 MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
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, Hi-C visualisation
Background The development over the last decade of high-throughput techniques to study the three-dimensional organisation of the genome [1–3] in the nucleus has fuelled the characterisation of chromatin conformation in a wide variety of biological systems. These range from the organisation of the bacterial nucleoid [4], to the in vitro characterisation of the molecular mechanisms that govern chromatin organisation in eukaryotes [5–10], reviewed in [11], how this organisation is dynamically regulated during cell cycle [12, 13], development and differentiation [14–19], reviewed in [20], and how it is affected in disease [21–23], reviewed in [24]. Given the fundamental role that the correct organisation of chromatin in the nucleus plays for proper cell physiology, there is a growing need to integrate chromatin contact data in current studies examining different aspects of gene and genome regulation. Different techniques have been developed to study chromatin conformation at the single cell or population level, in situ Hi-C being the primary method of choice for analysing chromatin conformation in cell populations [25], reviewed in [26] (Fig. 1a, left). © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licen
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