HiCrayon

HiCrayon facilitates the integration of 3D chromatin organization maps and 1D datasets by coloring chromatin contact map interactions according to 1D signal.

Key Features:

• Co-visualization: Integrates data from genomic assays directly into chromatin contact maps by coloring interactions according to 1D signal.
• Interactive visualization: Enables interactive exploration of 2D chromatin conformation with 1D genomic signals within the same matrix.
• Publication-ready output: Produces publication-ready images of integrated 3D chromatin organization and 1D genomic data.

Scientific Applications:

• Compartment calling assessment: Visualizes the effectiveness of compartment calling algorithms.
• ChIP-seq relationship analysis: Reveals relationships between ChIP-seq data and various features of chromatin organization.
• Loop characterization: Improves visualization of differences between loops associated with CTCF/cohesin versus those associated with H3K27ac.
• Differentiation studies: Visualizes organizational changes that occur during cellular differentiation.
• Novel compartment detection: Detects compartment patterns that cannot be assigned to either A or B compartments, revealing a distinct third chromatin compartment.

Methodology:

HiCrayon is implemented in R and Python.