HierarchicalHotNet

Julia implementation of Hierarchical HotNet algorithm for finding hotspots in
the altered networks.

Docs	Build	Test	DOI

The original Python implementation by RaphaelLab is available at hierarchical-hotnet GitHub repository.

In comparison to the original implementation, this Julia package includes a
few enhancements and additional functionality:

• optimizations and enhancements
  • reduced memory footprint
  • edge weights indexing for faster building of SCC tree
  • taking into account node in- and out-degree when reshuffling the node weights
    for randomized input data
• source-sink analysis for identifying paths from the set of source nodes to
  the sink nodes
• calculation of edge p-values using randomized networks
• export the network as data frames of vertices, edges and connected components

References

The Hierarchical HotNet paper:

M.A. Reyna, M.D.M. Leiserson, B.J. Raphael. Hierarchical HotNet: identifying hierarchies of altered subnetworks. ECCB/Bioinformatics 34(17):i972-980, 2018.