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Framework for systematic discovery of novel complexes and differential analysis of cofractionation MS datasets

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PCprophet

Software toolkit for protein complex prediction and differential analysis of cofractionation mass spectrometry datasets.

Getting Started

These instructions will guide you to obtain a copy of the project, to run on your local machine, and to test the compatibility with your current Python packages.

Dependencies

Installing

We recommend using anaconda as it contains the majority of the required packages for PCprophet. If you are using Windows and having problems adding paths of anaconda and Python, please click here for guidance. Please also refer to this page for potential errors when importing python packages in Windows.

Command line version

Ensure that you have installed the GitHub tool and 'git-lfs' command specifically for large file transfer. Please see here for installing GitHub and here for the installing 'git-lfs' command.

git-lfs clone https://github.com/anfoss/PCprophet PCprophet

This will get you a working copy of PCprophet into a folder called PCprophet. Please go to the 'PCprophet' folder to unzip 'tmp_GO_sp_only.txt.zip'. You then should be able to see the tmp_GO_sp_only.txt file in the same folder. Note that the 'tmp_GO_sp_only.txt' file must be under the 'PCprophet' folder.

Usage

For usage of PCprophet, refer to the PCprophet_instructions.md.

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Authors

License

This project is licensed under the MIT License - see the LICENSE.md file for details.

PCprophet citation:

Fossati, A., Li, C., Uliana, F., Wendt, F., Frommelt, F., Sykacek, P., Heusel, M., Hallal, M., Bludau, I., Capraz, T., Xue, P., Song, J., Wollscheid, B., Purcell, A. W., Gstaiger, M., & Aebersold, R. (2021). PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. Nature Methods, 13. https://doi.org/10.1038/s41592-021-01107-5

Acknowledgments

  • mojaje for the implementation of GO tree parsing.

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Framework for systematic discovery of novel complexes and differential analysis of cofractionation MS datasets

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