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README.md

Hetnet connectivity search prototyping and data repository

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Hetmech is a project to extract mechanistic connections between nodes in hetnets. The project aims to identify 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).

Note: the hetmech python package has been renamed to hetmatpy and relocated to hetio/hetmatpy. This repository is now used as a historical archive, as well as a dataset storage and method prototyping repository.

Many findings from this repository are described in the Connectivity Search Manuscript. The manuscript source code is available in greenelab/connectivity-search-manuscript.

Environment

This repository uses conda to manage its environment as specified in environment.yml. Install the environment with:

# install new hetmech environment
conda env create --file=environment.yml

# update existing hetmech environment
conda env update --file=environment.yml

Then use conda activate hetmech and conda deactivate to activate or deactivate the environment.

Acknowledgments

This work was supported through a research collaboration with Pfizer Worldwide Research and Development. This work was funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grants GBMF4552 to Casey Greene and GBMF4560 to Blair Sullivan.

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