motifcluster
Motif-based weighted spectral clustering in Python, R and Julia
Science Score: 23.0%
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○DOI references
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✓Academic publication links
Links to: arxiv.org -
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○Scientific vocabulary similarity
Low similarity (14.8%) to scientific vocabulary
Repository
Motif-based weighted spectral clustering in Python, R and Julia
Basic Info
Statistics
- Stars: 27
- Watchers: 5
- Forks: 3
- Open Issues: 0
- Releases: 7
Metadata Files
README.md
motifcluster 
Motif-based spectral clustering of weighted directed networks
Introduction
This repository provides implementations of motif-based spectral clustering of weighted directed networks in R, Python and Julia. This code is based on methods detailed in [Underwood, Elliott and Cucuringu, 2020], which is available at arXiv:2004.01293. These packages provide the capability for:
- Building motif adjacency matrices
- Sampling random weighted directed networks
- Spectral embedding with motif adjacency matrices
- Motif-based spectral clustering
The methods are all designed to run quickly on large sparse networks, and are easy to install and use.
Branches
The main branch contains stable versions. The develop branch may be unstable, and is for development purposes only.
Authors
- William George Underwood, Princeton University (Python, R, Julia, maintainer)
- Andrew Elliott, The Alan Turing Institute (Python)
License
This repository and its included R, Python and Julia packages are all licensed under GPLv3.
R package
The motifcluster R package is in the R directory.
Installation
The R package can be installed from CRAN with:
install.packages("motifcluster")
Dependencies
The R package has the following dependencies, available on CRAN:
- igraph
- Matrix
- RSpectra
Documentation
The package's manual is in the R/doc directory. R documentation files are provided for each function available in the package. An instructional vignette is in the R/vignettes directory.
Python package
The motifcluster Python package is in the python directory.
Installation
The Python package can be installed from PyPI with:
pip install motifcluster
Alternatively it can be installed with conda using:
conda install -c conda-forge motifcluster
Dependencies
The Python package has the following dependencies:
- Networkx
- Numpy
- Scipy
- Scikit-learn
Documentation
Full documentation is available at motifcluster.readthedocs.io.
Julia package
The MotifCluster Julia package is in the julia directory.
Installation
From the Julia General registry:
] add MotifCluster
Dependencies
- Aqua
- Clustering
- Distributions
- Graphs
Documentation
Documentation for the MotifCluster package is available on the web.
Performance
The performance directory contains scripts and plots relating to timing the construction of motif adjacency matrices, in R, Python and Julia.
Sticker
A high-resolution hexagonal sticker is available in the sticker directory.
Owner
- Name: William Underwood
- Login: WGUNDERWOOD
- Kind: user
- Location: USA
- Company: Princeton University
- Website: https://wgunderwood.github.io/
- Repositories: 3
- Profile: https://github.com/WGUNDERWOOD
PhD Student at Princeton University
GitHub Events
Total
- Watch event: 3
Last Year
- Watch event: 3
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| William G Underwood | 4****D | 474 |
| ande | a****t@g****m | 2 |
| Charles Twardy | 9****y | 1 |
| CompatHelper Julia | c****y@j****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 1
- Total pull requests: 3
- Average time to close issues: 4 days
- Average time to close pull requests: about 21 hours
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 2.0
- Average comments per pull request: 1.33
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 2
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- aaalissa (1)
Pull Request Authors
- github-actions[bot] (2)
- ctwardy (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 4
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Total downloads:
- pypi 700 last-month
- cran 337 last-month
- julia 1 total
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 1
(may contain duplicates) - Total versions: 21
- Total maintainers: 2
pypi.org: motifcluster
Motif-Based Spectral Clustering of Weighted Directed Networks
- Homepage: https://github.com/WGUNDERWOOD/motifcluster
- Documentation: https://motifcluster.readthedocs.io/
- License: GPLv3
-
Latest release: 0.2.3
published over 3 years ago
Rankings
Maintainers (1)
juliahub.com: MotifCluster
Motif-based weighted spectral clustering in Python, R and Julia
- Documentation: https://docs.juliahub.com/General/MotifCluster/stable/
- License: GPL-3.0
-
Latest release: 0.2.3
published about 3 years ago
Rankings
cran.r-project.org: motifcluster
Motif-Based Spectral Clustering of Weighted Directed Networks
- Homepage: https://github.com/wgunderwood/motifcluster
- Documentation: http://cran.r-project.org/web/packages/motifcluster/motifcluster.pdf
- License: GPL-3
-
Latest release: 0.2.3
published over 3 years ago
Rankings
Maintainers (1)
conda-forge.org: motifcluster
- Homepage: https://github.com/WGUNDERWOOD/motifcluster
- License: GPL-3.0-only
-
Latest release: 0.2.2
published almost 4 years ago
Rankings
Dependencies
- R >= 3.6.0 depends
- Matrix >= 1.2 imports
- RSpectra >= 0.16.0 imports
- igraph >= 1.2.5 imports
- covr >= 3.5.0 suggests
- knitr >= 1.28 suggests
- mclust >= 5.4.6 suggests
- rmarkdown >= 2.1 suggests
- testthat >= 2.3.2 suggests
- coverage >=4.5.4
- networkx >=2.4
- numpy >=1.18.3
- pylint >=2.11.1
- pytest-cov >=2.8.1
- scikit-learn >=0.22.2
- scipy >=1.4.1
- networkx >=2.4
- numpy >=1.18.3
- scikit-learn >=0.22.2
- scipy >=1.4.1