mariner

mariner extracts, aggregates, and visualizes chromatin interaction data from Hi-C matrices within the R/Bioconductor environment.

Key Features:

• Paired ranges manipulation: Manipulates and merges paired genomic regions.
• Paired ranges generation: Generates paired ranges for Hi-C analysis.
• Hi-C data extraction: Extracts interactions from .hic files using a parallel and block-processing approach.
• Interaction aggregation: Aggregates Hi-C contacts from multiple files.
• Visualization integration: Visualizes results with compatibility for plotgardener.
• Modular workflow: Provides modular functions for customization and all-in-one functions for common analyses.
• Bioconductor integration: Integrates with existing Bioconductor infrastructure for complete Hi-C analysis in R.

Scientific Applications:

• 3D chromatin architecture analysis: Enables investigation of chromatin structure and its role in gene expression regulation.
• Hi-C data querying: Facilitates extraction of contacts from multiple Hi-C files for downstream analysis.
• Chromatin interaction visualization: Supports plotting of Hi-C interaction data for interpretation of 3D genome organization.

Methodology:

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