HiCeekR: A Novel Shiny App for Hi-C Data Analysis
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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-11-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.01079/full |
| _version_ | 1818846599169703936 |
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| author | Lucio Di Filippo Dario Righelli Miriam Gagliardi Miriam Gagliardi Maria Rosaria Matarazzo Claudia Angelini |
| author_facet | Lucio Di Filippo Dario Righelli Miriam Gagliardi Miriam Gagliardi Maria Rosaria Matarazzo Claudia Angelini |
| author_sort | Lucio Di Filippo |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-19T05:48:07Z |
| format | Article |
| id | doaj.art-ddc18dd9238147bb8aa971be67d5ca6f |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-19T05:48:07Z |
| publishDate | 2019-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-ddc18dd9238147bb8aa971be67d5ca6f2022-12-21T20:33:45ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-11-011010.3389/fgene.2019.01079486028HiCeekR: A Novel Shiny App for Hi-C Data AnalysisLucio Di Filippo0Dario Righelli1Miriam Gagliardi2Miriam Gagliardi3Maria Rosaria Matarazzo4Claudia Angelini5Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, ItalyIstituto per le Applicazioni del Calcolo “Mauro Picone,” Consiglio Nazionale delle Ricerche, Napoli, ItalyMax Planck Institute for Psychiatry, Munich, GermanyInstitute of Genetics and Biophysics “A. Buzzati A. Traverso,” Consiglio Nazionale delle Ricerche, Napoli, ItalyInstitute of Genetics and Biophysics “A. Buzzati A. Traverso,” Consiglio Nazionale delle Ricerche, Napoli, ItalyIstituto per le Applicazioni del Calcolo “Mauro Picone,” Consiglio Nazionale delle Ricerche, Napoli, ItalyThe 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.https://www.frontiersin.org/article/10.3389/fgene.2019.01079/fullHi-Cuser-friendly interfacelong-range interactionsgenome organizationtopologically associating domains |
| spellingShingle | Lucio Di Filippo Dario Righelli Miriam Gagliardi Miriam Gagliardi Maria Rosaria Matarazzo Claudia Angelini HiCeekR: A Novel Shiny App for Hi-C Data Analysis Frontiers in Genetics Hi-C user-friendly interface long-range interactions genome organization topologically associating domains |
| title | HiCeekR: A Novel Shiny App for Hi-C Data Analysis |
| title_full | HiCeekR: A Novel Shiny App for Hi-C Data Analysis |
| title_fullStr | HiCeekR: A Novel Shiny App for Hi-C Data Analysis |
| title_full_unstemmed | HiCeekR: A Novel Shiny App for Hi-C Data Analysis |
| title_short | HiCeekR: A Novel Shiny App for Hi-C Data Analysis |
| title_sort | hiceekr a novel shiny app for hi c data analysis |
| topic | Hi-C user-friendly interface long-range interactions genome organization topologically associating domains |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.01079/full |
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