HiCExplorer

HiCExplorer performs reproducible preprocessing, analysis, and visualization of Hi-C, Capture Hi-C (cHi-C), and single-cell Hi-C (scHi-C) datasets to study three-dimensional genome organization.

Key Features:

• Data Pre-processing and Analysis: Performs preprocessing and analysis of large-scale Hi-C chromosome conformation datasets.
• Capture Hi-C (cHi-C) Tools: Provides expanded functionalities for Capture Hi-C (cHi-C) analysis to investigate specific genomic regions.
• Single-cell Hi-C (scHi-C) Analysis: Supports single-cell Hi-C (scHi-C) data analysis to explore chromosomal interactions and cellular heterogeneity.
• Visualization Capabilities: Includes robust visualization options for interpreting complex chromosome interaction datasets.

Scientific Applications:

• Epigenetics: Analysis of how chromosomal interactions influence gene regulation.
• Developmental Biology: Investigation of changes in genome organization during development.
• Disease Research: Identification of structural variations and aberrant chromosomal interactions associated with diseases such as cancer.

Methodology:

Computational steps explicitly include preprocessing, analysis, and visualization of Hi-C, cHi-C, and scHi-C datasets.