https://github.com/alyst/hierarchicalhotnet.jl

Julia implementation of Hierarchical HotNet method
https://github.com/alyst/hierarchicalhotnet.jl

biological-networks hierarchical-clustering hierarchical-hotnet julia-package random-walk weighted-graphs

Last synced: 9 months ago
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Julia implementation of Hierarchical HotNet method

• Host: GitHub
• URL: https://github.com/alyst/hierarchicalhotnet.jl
• Owner: alyst
• Created: 2020-03-03T14:23:48.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2024-05-06T00:56:27.000Z (over 1 year ago)
• Last Synced: 2025-01-21T06:44:12.795Z (11 months ago)
• Topics: biological-networks, hierarchical-clustering, hierarchical-hotnet, julia-package, random-walk, weighted-graphs
• Language: Julia
• Size: 658 KB
• Stars: 2
• Watchers: 3
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

          
# HierarchicalHotNet

Julia implementation of *Hierarchical HotNet* algorithm for finding hotspots in

the altered networks.

| Docs | Build | Test | DOI |

|:-----|:------|:-----|:----|

| [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://alyst.github.io/HierarchicalHotNet.jl/dev) | [![Build Status](https://github.com/alyst/HierarchicalHotNet.jl/workflows/CI/badge.svg)](https://github.com/alyst/HierarchicalHotNet.jl/actions?query=workflow%3ACI+branch%3Amaster) | [![Codecov](https://codecov.io/gh/alyst/HierarchicalHotNet.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/alyst/HierarchicalHotNet.jl) | [![DOI](https://zenodo.org/badge/244656363.svg)](https://zenodo.org/badge/latestdoi/244656363) |

The original *Python* implementation by [RaphaelLab](http://compbio.cs.brown.edu/) is available at [hierarchical-hotnet](https://github.com/raphael-group/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*](https://alyst.github.io/HierarchicalHotNet.jl/dev/source_sink.html) 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](https://academic.oup.com/bioinformatics/article/34/17/i972/5093236), 2018.