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

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-co...

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Detalles Bibliográficos
Autores principales: Kruse, Kai, Hug, Clemens B., Vaquerizas, Juan M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7745377/
https://www.ncbi.nlm.nih.gov/pubmed/33334380
http://dx.doi.org/10.1186/s13059-020-02215-9
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author Kruse, Kai
Hug, Clemens B.
Vaquerizas, Juan M.
author_facet Kruse, Kai
Hug, Clemens B.
Vaquerizas, Juan M.
author_sort Kruse, Kai
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-020-02215-9.
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spelling pubmed-77453772020-12-18 FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data Kruse, Kai Hug, Clemens B. Vaquerizas, Juan M. Genome Biol Software 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-020-02215-9. BioMed Central 2020-12-17 /pmc/articles/PMC7745377/ /pubmed/33334380 http://dx.doi.org/10.1186/s13059-020-02215-9 Text en © The Author(s) 2020 Open AccessThis 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 licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Kruse, Kai
Hug, Clemens B.
Vaquerizas, Juan M.
FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
title FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
title_full FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
title_fullStr FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
title_full_unstemmed FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
title_short FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
title_sort fan-c: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7745377/
https://www.ncbi.nlm.nih.gov/pubmed/33334380
http://dx.doi.org/10.1186/s13059-020-02215-9
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