PathwayAnalysis is a Python library designed to do the following two tasks.

• Compute pathway expression data from gene expression data. See the in review paper Pathway Expression Analysis
• Identify small discriminatory gene co-expression modules using spectral hierarchical clustering using a modified version of the iterative spectral clustering algorithm in Methods for Network Generation and Spectral Feature Selection: Especially on Gene Expression Data

If you like the pathway expression code, please consider citing us.

@article{mankovich2022pathway,
  title={Pathway expression analysis},
  author={Mankovich, Nathan and Kehoe, Eric and Peterson, Amy and Kirby, Michael},
  journal={Scientific Reports},
  volume={12},
  number={1},
  pages={21839},
  year={2022},
  publisher={Nature Publishing Group UK London}
}

If you like the spectral clustering code, please consider citing us.

@phdthesis{mankovich2019methods,
  title={Methods for Network Generation and Spectral Feature Selection: Especially on Gene Expression Data},
  author={Mankovich, Nathan},
  year={2019},
  school={Colorado State University}
}

To install PathwayAnalysis, python version 3.8 or greater is required. All other required packages and versions can be found in requirements.txt.

git cloning the PathwayAnalysis, going to the PathwayAnalysis directory, run

pip install -e .

See the jupyter notebooks in the folder ./examples