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https://github.com/greenelab/xswap-analysis
Analysis and experiments for https://github.com/greenelab/xswap-manuscript
https://github.com/greenelab/xswap-analysis
degree edge-prior hetnets networks notebooks permutation software tool xswap
Last synced: 2 months ago
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Analysis and experiments for https://github.com/greenelab/xswap-manuscript
- Host: GitHub
- URL: https://github.com/greenelab/xswap-analysis
- Owner: greenelab
- License: bsd-3-clause
- Created: 2018-12-03T19:55:44.000Z (about 6 years ago)
- Default Branch: main
- Last Pushed: 2023-12-29T16:53:54.000Z (about 1 year ago)
- Last Synced: 2024-05-02T06:00:23.638Z (9 months ago)
- Topics: degree, edge-prior, hetnets, networks, notebooks, permutation, software, tool, xswap
- Language: Jupyter Notebook
- Homepage:
- Size: 116 MB
- Stars: 3
- Watchers: 6
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Analysis and figure generation for XSwap project
This repository hosts notebooks, images, and data for the XSwap project.
The results of these analyses are described in the manuscript titled:
[**The probability of edge existence due to node degree: a baseline for network-based predictions**](https://github.com/greenelab/xswap-manuscript/)
Along with the manuscript, this project produced an open-source implementation of our network permutation algorithm.
Available on PyPI as [`xswap`](https://pypi.org/project/xswap/) and source on GitHub in [hetio/xswap](https://github.com/hetio/xswap/).
## Layout
The analyses for this repository are performed by sequentially numbered Jupyter notebooks in the [`nb`](nb) directory.
Data is written to the [`data`](data) directory and figures are exported to the [`img`](img) directory.
The analyses depend on the [Hetionet HetMat dataset](https://github.com/hetio/hetionet/tree/master/hetnet/matrix),
which can be downloaded by running the following Python command from this repo's root directory:
```py
from hetmatpy.hetmat.archive import load_archive
load_archive(
archive_path="https://github.com/hetio/hetionet/raw/b467b8b41087288390b41fdb796577ada9f03bda/hetnet/matrix/hetionet-v1.0.hetmat.zip",
destination_dir="data/task1/hetionet-v1.0.hetmat",
)
```
## Environment
This repository uses [conda](http://conda.pydata.org/docs/) to manage its environment as specified in [`environment.yml`](environment.yml).
Install the environment with:
```sh
# install new xswap-analysis environment
conda env create --file=environment.yml
# update existing xswap-analysis environment
conda env update --file=environment.yml
# export the locked environment specification, which lists every package
# installed in the environment including implicit dependencies.
# Includes build numbers and is operating system specific.
conda env export --name=xswap-analysis > environment-lock-linux.yml
```
Then use `conda activate xswap-analysis` and `conda deactivate` to activate or deactivate the environment.
## License
The entire repository is released under a [BSD 3-Clause License](LICENSE).
Furthermore:
- the contents of the [`data`](data) directory are released under [CC0](https://creativecommons.org/publicdomain/zero/1.0/) (public domain dedication).
- the contents of the [`img`](img) directory are released under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) (public domain dedication).
For images that are used in the [xswap-manuscript](https://github.com/greenelab/xswap-manuscript/),
please attribute this manuscript as the source.