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https://github.com/biocypher/graphpack

A Python tool to perform graph compression and visualization

https://github.com/biocypher/graphpack

Science Score: 13.0%

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    CITATION.cff file
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    Scientific vocabulary similarity
    Low similarity (11.0%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

A Python tool to perform graph compression and visualization

Basic Info
  • Host: GitHub
  • Owner: biocypher
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 5.98 MB
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

Description

GraphPack is a Python tool engineered to facilitate the compression and visualization of large-scale networks, such as protein-protein interaction (PPI) networks or metabolic pathways. It offers a user-friendly interface that enables the application of diverse graph compression algorithms and the visualization of the original and compressed networks.

GraphPack provides flexibility in how you interact with it, supporting both command-line interface (CLI) usage with arguments and integration into Python applications via an API.

The tool supports both weighted and unweighted graphs, allowing users to analyze a wide range of network types. It is specifically designed to handle large-scale, biological networks such as protein-protein interaction (PPI) networks, gene regulatory networks,and metabolic pathways, but can be applied to any network data.

Detailed Description

GraphPack includes a variety of graph compression algorithms to choose from:

  • Louvain Clustering
  • Greedy Algorithm
  • Label Propagation
  • Asynchronous Fluid Communities
  • Spectral Clustering
  • Hierarchical Clustering
  • Node2Vec
  • DeepWalk
  • Clique Percolation Method (CPM)
  • Non-negative Matrix Factorization (NMF)

GraphPack generates mapping files that maintain the relationship between the original and compressed nodes. This ensures that the compressed network can be decompressed to the original network without any loss of information, in case of lossless compression, or in any case that information about the relationship between the new nodes and the old nodes is available.

GraphPack provides robust visualization options for both the original and compressed networks, facilitating easy comparison and in-depth analysis.

Installation

Install GraphPack from PyPI via:

bash pip install graphpack

License

This project is licensed under the MIT License.

Owner

  • Name: biocypher
  • Login: biocypher
  • Kind: organization

GitHub Events

Total
  • Issues event: 9
  • Watch event: 1
  • Issue comment event: 4
  • Member event: 2
Last Year
  • Issues event: 9
  • Watch event: 1
  • Issue comment event: 4
  • Member event: 2

Issues and Pull Requests

Last synced: 11 months ago

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Past Year
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Top Authors
Issue Authors
  • ecarrenolozano (4)
Pull Request Authors
Top Labels
Issue Labels
good first issue (1)
Pull Request Labels

Dependencies

pyproject.toml pypi
  • gensim ~4.3.2
  • gseapy ~1.1.0
  • matplotlib ~3.6.3
  • msgpack ~1.0.7
  • networkx ~2.8.8
  • node2vec ~0.4.6
  • numpy ~1.26.2
  • pandas ~2.2.1
  • plotly ~5.22.0
  • python >=3.10,<3.11
  • python-louvain ~0.16
  • pyvis ~0.3.1
  • requests ~2.31.0
  • scikit-learn ~1.4.1.post1
  • scipy 1.11.4
  • tqdm ~4.66.1