GITAR

GITAR analyzes Hi-C genomic interaction data to generate intra-chromosomal contact matrices and topologically-associated domain (TAD) coordinates for studying chromatin organization.

Key Features:

• Two-Module Architecture: Composed of HiCtool (a Python library for Hi-C data processing and visualization) and a Processed Data Library of pre-processed datasets.
• HiCtool: Processes raw Hi-C data and provides tools for analysis and visualization, including topologically-associated domain (TAD) analysis.
• Processed Data Library: Contains standardized pre-processed human and mouse Hi-C datasets for consistent cross-study comparison.
• Comprehensive Workflow: Transforms raw Hi-C data into optimized intra-chromosomal contact matrices and TAD coordinates via preprocessing, normalization, and visualization.
• Standardization and Efficiency: Provides ready-to-use standardized datasets to support reproducible downstream analyses and comparative studies.

Scientific Applications:

• Chromatin interaction mapping: Analysis of chromatin interactions and genome organization through identification of TADs and contact matrices.
• Functional genomics: Integration with functional genomic assays to investigate genomic regulation and structural organization.
• Comparative genomics: Cross-study and cross-species comparisons using standardized human and mouse Hi-C datasets.

Methodology:

HiCtool processes raw Hi-C data through preprocessing, normalization, and visualization to produce intra-chromosomal contact matrices and TAD coordinates, while the Processed Data Library provides pre-processed human and mouse Hi-C datasets.