GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data / 基因组蛋白质组与生物信息学报·英文版
Genomics, Proteomics & Bioinformatics
;
(4): 365-372, 2018.
Article
in English
| WPRIM
| ID: wpr-772971
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.
Full text:
Available
Index:
WPRIM (Western Pacific)
Main subject:
Computer Graphics
/
Software
/
Chromatin
/
Chemistry
/
Genome
/
Genomics
/
Methods
Limits:
Animals
/
Humans
Language:
English
Journal:
Genomics, Proteomics & Bioinformatics
Year:
2018
Type:
Article
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