HiCeekR

HiCeekR provides comprehensive analysis of Hi-C (High-throughput Chromosome Conformation Capture) data from Next Generation Sequencing to identify chromatin loops, topologically associating domains (TADs), and A/B compartments and to integrate these data with other omic layers for studying 3D genome organization.

Key Features:

• Hi-C data processing: Implements a pipeline spanning pre-processing to visualization of Hi-C datasets.
• Hi-C / NGS support: Operates on Hi-C data generated by Next Generation Sequencing and the High-throughput Chromosome Conformation Capture technique.
• R/Bioconductor integration: Integrates multiple R/Bioconductor packages for downstream analyses.
• Chromatin loop detection: Identifies chromatin loops from Hi-C contact data.
• TAD identification: Detects topologically associating domains (TADs).
• A/B compartment calling: Calls A/B compartments to characterize large-scale chromatin states.
• Multi-omics integration: Integrates and visualizes additional omic layers alongside Hi-C data for multi-omics analyses.
• Public dataset application: Has been applied to publicly available datasets to demonstrate functionality.

Scientific Applications:

• 3D genome organization analysis: Studying genome-wide 3D chromatin architecture through detection of loops, TADs, and compartments.
• Multi-omics correlation: Correlating chromatin structure with other omic datasets to investigate relationships between genome architecture and function.
• Reanalysis of public Hi-C data: Reanalyzing publicly available Hi-C datasets for comparative or validation studies.

Methodology:

Performs pre-processing through visualization of Hi-C data, integrates multiple R/Bioconductor packages, and executes chromatin loop, TAD, and A/B compartment identification on Hi-C data generated by Next Generation Sequencing; analyses have been demonstrated on publicly available datasets.