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HierarchicalHotNet

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

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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.