Back to Search
Start Over
GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data.
- Source :
-
Genomics, proteomics & bioinformatics [Genomics Proteomics Bioinformatics] 2018 Oct; Vol. 16 (5), pp. 365-372. Date of Electronic Publication: 2018 Dec 13. - Publication Year :
- 2018
-
Abstract
- Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome. Among these methods, Hi-C plays a key role. Here, we present the Genome Interaction Tools and Resources (GITAR), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, and visualization, as well as analysis of topologically-associated domains (TADs). GITAR is composed of two main modules: (1) HiCtool, a Python library to process and visualize Hi-C data, including TAD analysis; and (2) processed data library, a large collection of human and mouse datasets processed using HiCtool. HiCtool leads the user step-by-step through a pipeline, which goes from the raw Hi-C data to the computation, visualization, and optimized storage of intra-chromosomal contact matrices and TAD coordinates. A large collection of standardized processed data allows the users to compare different datasets in a consistent way, while saving time to obtain data for visualization or additional analyses. More importantly, GITAR enables users without any programming or bioinformatic expertise to work with Hi-C data. GITAR is publicly available at http://genomegitar.org as an open-source software.<br /> (Copyright © 2018 The Authors. Production and hosting by Elsevier B.V. All rights reserved.)
Details
- Language :
- English
- ISSN :
- 2210-3244
- Volume :
- 16
- Issue :
- 5
- Database :
- MEDLINE
- Journal :
- Genomics, proteomics & bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 30553884
- Full Text :
- https://doi.org/10.1016/j.gpb.2018.06.006