MCPNetPaper2022

This repository contains the scripts used to generate the tables in the paper.

For completeness, it includes the MCPNet code as a git submodule. To retrieve the code, please call from the source directory

git submodule update --init --recursive

Please see https://github.com/AluruLab/MCPNet for more information about building and running the code.

Script organization

The scripts directory include python, R, and bash shell scripts.

• directory simulate_with_noise: contains scripts for generating the simulated yeast data and injecting random noise.

For MCPNet

• directory eval_params: contains scripts for parameter evaluations for Supplemental Material S1.2

• mcpnet_simulated_eval.sh: slurm script to run mcpnet for all simulated yeast, noisy or noise-free, datasets

• mcpnet_arabidopsis_eval.pbs: pbs script to run mcpnet for athaliana datasets

• mcpnet_yeast_eval.pbs and mcpnet_yeast_eval_1core.pbs: pbs scripts to run mcpnet for real yeast dataset.

For Existing Tools

• directory ath_json: contains parameters for evaluating AUPR for all athaliana data sets and all existing tools.

• athaliana_auc_pr.py: computes the AUPR for all athaliana data sets and all existing tools.

• simulated_input.json and simulated_roc_pr.py: computes the AUPR for simulated noisy yeast data for all existing tools.

• yeast_input.json and yeast_ath_roc_pr.py: computes the AUPR for real yeast and the development athaliana datasets for all existing tools.