{"id":20074694,"url":"https://github.com/greenelab/xswap-analysis","last_synced_at":"2025-05-05T21:32:04.863Z","repository":{"id":77783376,"uuid":"160245899","full_name":"greenelab/xswap-analysis","owner":"greenelab","description":"Analysis and experiments for https://github.com/greenelab/xswap-manuscript","archived":false,"fork":false,"pushed_at":"2023-12-29T16:53:54.000Z","size":121342,"stargazers_count":3,"open_issues_count":1,"forks_count":1,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-04-09T04:41:40.636Z","etag":null,"topics":["degree","edge-prior","hetnets","networks","notebooks","permutation","software","tool","xswap"],"latest_commit_sha":null,"homepage":"","language":"Jupyter 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Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Analysis and figure generation for XSwap project\n\nThis repository hosts notebooks, images, and data for the XSwap project.\nThe results of these analyses are described in the manuscript titled:\n\n[**The probability of edge existence due to node degree: a baseline for network-based predictions**](https://github.com/greenelab/xswap-manuscript/)\u003cbr\u003e\n\nAlong with the manuscript, this project produced an open-source implementation of our network permutation algorithm.\nAvailable on PyPI as [`xswap`](https://pypi.org/project/xswap/) and source on GitHub in [hetio/xswap](https://github.com/hetio/xswap/).\n\n## Layout\n\nThe analyses for this repository are performed by sequentially numbered Jupyter notebooks in the [`nb`](nb) directory.\nData is written to the [`data`](data) directory and figures are exported to the [`img`](img) directory.\n\nThe analyses depend on the [Hetionet HetMat dataset](https://github.com/hetio/hetionet/tree/master/hetnet/matrix),\nwhich can be downloaded by running the following Python command from this repo's root directory:\n\n```py\nfrom hetmatpy.hetmat.archive import load_archive\nload_archive(\n    archive_path=\"https://github.com/hetio/hetionet/raw/b467b8b41087288390b41fdb796577ada9f03bda/hetnet/matrix/hetionet-v1.0.hetmat.zip\",\n    destination_dir=\"data/task1/hetionet-v1.0.hetmat\",\n)\n```\n\n## Environment\n\nThis repository uses [conda](http://conda.pydata.org/docs/) to manage its environment as specified in [`environment.yml`](environment.yml).\nInstall the environment with:\n\n```sh\n# install new xswap-analysis environment\nconda env create --file=environment.yml\n\n# update existing xswap-analysis environment\nconda env update --file=environment.yml\n\n# export the locked environment specification, which lists every package\n# installed in the environment including implicit dependencies.\n# Includes build numbers and is operating system specific.\nconda env export --name=xswap-analysis \u003e environment-lock-linux.yml\n```\n\nThen use `conda activate xswap-analysis` and `conda deactivate` to activate or deactivate the environment.\n\n## License\n\nThe entire repository is released under a [BSD 3-Clause License](LICENSE).\nFurthermore:\n\n- the contents of the [`data`](data) directory are released under [CC0](https://creativecommons.org/publicdomain/zero/1.0/) (public domain dedication).\n- the contents of the [`img`](img) directory are released under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) (public domain dedication).\n  For images that are used in the [xswap-manuscript](https://github.com/greenelab/xswap-manuscript/),\n  please attribute this manuscript as the source.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fxswap-analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgreenelab%2Fxswap-analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fxswap-analysis/lists"}