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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.01079

HiCeekR: a novel Shiny app for Hi-C data analysis.

  • 1Telethon Institute Of Genetics And Medicine, Italy
  • 2Istituto per le applicazioni del calcolo 'Mauro Picone' (IAC), Italy
  • 3Max Planck Institute of Psychiatry (MPI), Germany
  • 4Institute of Genetics and Biophysics (CNR), Italy
  • 5Istituto per le applicazioni del calcolo "Mauro Picone" (IAC), Italy

The High-throughput Chromosome Conformation Capture (Hi-C) technique combines the power of the Next Generation Sequencing technologies with chromosome conformation capture approach to study the 3D chromatin organization at the genome-wide scale.
Although such a technique is quite recent, many tools are already available for pre-processing and analyzing Hi-C data, allowing to identify chromatin loops, topological associating domains and A/B compartments.
However, only a few of them provide an exhaustive analysis pipeline or allow to easily integrate and visualize other omic layers.
Moreover, most of the available tools are designed for expert users, who have great confidence with command-line applications.
In this paper, we present HiCeekR (\url{}), a novel R Graphical User Interface (GUI) that allows researchers to easily perform a complete Hi-C data analysis.
With the aid of the Shiny libraries, it integrates several R/Bioconductor packages for Hi-C data analysis and visualization, guiding the user during the entire process.
Here, we describe its architecture and functionalities, then illustrate its capabilities using a publicly available dataset.

Keywords: Hi-C, User-friendly interface, long-range interaction, genome organization, Topological associated domains

Received: 19 Jul 2019; Accepted: 09 Oct 2019.

Copyright: © 2019 Di Filippo, Righelli, Gagliardi, Matarazzo and Angelini. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: PhD. Claudia Angelini, Istituto per le applicazioni del calcolo "Mauro Picone" (IAC), Rome, Italy,