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What is Higashi

Multiscale and integrative single-cell Hi-C analysis with Higashi

Higashi is a computational framework for scHi-C analysis with the following features:

• Higashi represents the scHi-C dataset as a hypergraph
  • Each cell and each genomic bin are represented as the cell node and the genomic bin node.
  • Each non-zero entry in the single-cell contact map is modeled as a hyperedge.
  • The read count for each chromatin interaction is used as the attribute of the hyperedge.
• Higashi uses a hypergraph neural network to unveil high-order interaction patterns within this constructed hypergraph.
• Higashi can produce the embeddings for the scHi-C for downstream analysis.
• Higashi can impute single-cell Hi-C contact maps, enabling detailed characterization of 3D genome features such as TAD-like domain boundaries and A/B compartment scores at single-cell resolution.

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Follow the links below to get started:

• Installing Higashi
• Input File Format
• Higashi Usage
• Output Files