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https://github.com/hetio/hetmatpy

Python package for matrix storage and operations on hetnets
https://github.com/hetio/hetmatpy

greenelab hetio hetmat hetnet-connectivity-search hetnets matrix numpy python scipy

Last synced: 2 months ago
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Python package for matrix storage and operations on hetnets

Host: GitHub
URL: https://github.com/hetio/hetmatpy
Owner: hetio
License: other
Created: 2018-11-07T18:46:12.000Z (about 6 years ago)
Default Branch: main
Last Pushed: 2023-03-30T12:46:22.000Z (over 1 year ago)
Last Synced: 2024-10-01T14:58:00.982Z (3 months ago)
Topics: greenelab, hetio, hetmat, hetnet-connectivity-search, hetnets, matrix, numpy, python, scipy
Language: Python
Homepage:
Size: 1.36 MB
Stars: 14
Watchers: 3
Forks: 9
Open Issues: 2
Metadata Files:
- Readme: README.md
- License: LICENSE.md
- Citation: CITATION.cff

Awesome Lists containing this project

README

        # hetmatpy: a Python 3 package for matrix operations of hetnets

[![Documentation](https://img.shields.io/badge/-Documentation-purple?logo=read-the-docs&style=for-the-badge)](https://hetio.github.io/hetmatpy/)

[![PyPI](https://img.shields.io/pypi/v/hetmatpy.svg?logo=PyPI&style=for-the-badge)](https://pypi.org/project/hetmatpy/)

[![GitHub Actions CI Build Status](https://img.shields.io/github/actions/workflow/status/hetio/hetmatpy/test.yaml?branch=main&label=actions&style=for-the-badge&logo=github&logoColor=white)](https://github.com/hetio/hetmatpy/actions)

[![Bio Tools Badge](https://img.shields.io/badge/biotools-hetmatpy-lightgray?style=for-the-badge)](https://bio.tools/hetmatpy)

[![SciCrunch RRID Badge](https://img.shields.io/badge/RRID-SCR__023409-lightgray?style=for-the-badge)](https://scicrunch.org/resolver/RRID:SCR_023409)

This codebase enables identifying the relevant network connections between a set of query nodes.

The method is designed to operate on hetnets (networks with multiple node or relationship types).

This project is still under development.

Use with caution.

## Environment

Install via pip from GitHub using:

```shell

# install the latest release from PyPI

pip install hetmatpy

# install latest version on GitHub

pip install git+https://github.com/hetio/hetmatpy

# for local development, run the following inside the development environment:

pip install --editable .

```

## Development

This repo uses pre-commit checks:

```shell

# run once per local repo before committing

pre-commit install

```

## Acknowledgments

This work is supported through a research collaboration with [Pfizer Worldwide Research and Development](https://www.pfizer.com/partners/research-and-development).

This work is funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grants [GBMF4552](https://www.moore.org/grant-detail?grantId=GBMF4552) to Casey Greene and [GBMF4560](https://www.moore.org/grant-detail?grantId=GBMF4560) to Blair Sullivan.