script for metrics calculation

[theinvisibleliya]

The idea is to use F1 score metric to compare the outputs of the GRN-prioritizing perturbation models with experimental data (for example). Create a script that takes as input the GRN outputs and experimental data and outputs the F1 score metric.

The metric was used a lot in the SCENIC+ paper, see Fig. 3 and Extended Data Fig.4.: https://www.nature.com/articles/s41592-023-01938-4/figures/3 https://www.nature.com/articles/s41592-023-01938-4/figures/10

[marinaEM]

Contribution Guidelines

1. Initial Setup

   • Clone the repository: git clone <repository_url>

2. Update Local Content

   • Ensure you’re up to date with the development branch:

     git checkout devel
     git pull origin devel

3. Create a New Branch

   • Create a descriptive branch for your work:

     git checkout -b <branch_name>

4. Commit & Push Changes

   • Stage and commit your changes with clear messages:

     git add <file_name>
     git commit -m "Brief description of changes"

   • Push to GitHub:

     git push origin <branch_name>

5. Create a Pull Request

   • Target the devel branch for merging.
   • Follow the PR template, review, and submit.

6. Final Merge & Update

   • Once approved, merge your PR and delete your branch if desired.
   • Update your local repository:

     git checkout devel
     git pull origin devel

By following these steps, you contribute effectively and collaboratively.

[dlopez-bioinfo]

All metrics can be implemented in a single script with pertpy framework:

• input: prediction results, kind of metric
• output: metric results