cooltools

cooltools analyzes high-resolution Hi-C and other chromosome conformation capture (3C) contact frequency data to characterize genome architecture across cell types, states, and organisms.

Key Features:

• High-resolution contact map analysis: Provides computational routines for analyzing contact frequency maps generated by Hi-C and other 3C technologies.
• Scalability: Implements approaches to accommodate large-scale, high-resolution Hi-C datasets without prohibitive memory or storage constraints.
• Reproducibility: Emphasizes reproducible analysis practices to produce consistent results across computational environments.
• Cooler format integration: Leverages the cooler file format for storage and access of high-resolution Hi-C contact matrices.

Scientific Applications:

• Genome architecture profiling: Characterizes genome organization and contact frequency changes across different cell states and cell types using Hi-C data.
• Comparative genomics: Enables comparative analysis of chromatin folding and contact patterns across diverse organisms.
• Regulation and expression studies: Supports investigation of how three-dimensional genomic folding influences gene regulation and expression.

Methodology:

Operates on cooler-format files to store and access high-resolution Hi-C contact matrices and performs computational analysis of contact frequency maps from 3C technologies.