English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  HiCeekR: A Novel Shiny App for Hi-C Data Analysis

Di Filippo, L., Righelli, D., Gagliardi, M., Matarazzo, M. R., & Angelini, C. (2019). HiCeekR: A Novel Shiny App for Hi-C Data Analysis. Frontiers in Genetics, 10: 1079. doi:10.3389/fgene.2019.01079.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/21.11116/0000-0005-FAB7-3 Version Permalink: http://hdl.handle.net/21.11116/0000-0005-FAB8-2
Genre: Journal Article

Files

show Files

Locators

show

Creators

show
hide
 Creators:
Di Filippo, Lucio, Author
Righelli, Dario, Author
Gagliardi, Miriam1, 2, Author              
Matarazzo, Maria Rosaria, Author
Angelini, Claudia, Author
Affiliations:
1Max Planck Institute of Psychiatry, Max Planck Society, ou_1607137              
2RG Genomics of Complex Diseases, Max Planck Institute of Psychiatry, Max Planck Society, ou_3008285              

Content

show
hide
Free keywords: -
 Abstract: 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 (https://github.com/lucidif/HiCeekR), 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.

Details

show
hide
Language(s):
 Dates: 2019-11-04
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: ISI: 000497724800001
DOI: 10.3389/fgene.2019.01079
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Frontiers in Genetics
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: Lausanne : Frontiers Media
Pages: - Volume / Issue: 10 Sequence Number: 1079 Start / End Page: - Identifier: ISSN: 1664-8021
CoNE: https://pure.mpg.de/cone/journals/resource/1664-8021