mariner

mariner enables rapid, memory-efficient extraction, aggregation, and visualization of chromatin interaction data from Hi-C matrices within the R/Bioconductor environment.

Key Features:

• Parallel block-processing: Queries and extracts contacts from multiple Hi-C files using a parallel and block-processing approach for efficiency.
• Modular workflow functions: Provides modular functions for complete workflow customization alongside all-in-one functions for common analysis types.
• Bioconductor integration: Tight integration with existing Bioconductor infrastructure enables complete analysis and visualization of Hi-C data in R.
• Data manipulation: Supports manipulating, extracting, and aggregating chromatin interaction data from Hi-C datasets.

Scientific Applications:

• 3D chromatin architecture analysis: Facilitates investigation of Hi-C and Micro-C data to study 3D chromatin structure and its role in gene expression regulation.
• Disease-related chromatin alteration studies: Supports analysis of alterations to 3D chromatin structure associated with developmental abnormalities and disease.

Methodology:

mariner uses a parallel and block-processing approach for querying and extracting contacts from multiple Hi-C files.