README.md

Natural products have increased rates of clinical trial success throughout the drug development process

This repository contains code and data described in detail in our paper (Domingo-Fernández et al., 2024).

Table of Contents

• Citation
• Reproducibility
• Data

Citation

If you have found our manuscript useful in your work, please consider citing:

Domingo-Fernandez, D., Gadiya, Y., Preto, A. J., Krettler, C., Mubeen, S., Allen, A., Healey, D., Colluru, V. (2024). Natural products have increased rates of clinical trial success throughout the drug development process. bioRxiv.

Reproducibility

Set up the environment (Python)

Install requirements

python -m venv .venv && source ./.venv/bin/activate
pip install -r requirements.txt

Rerun the notebooks

Run the notebooks located in the notebooks corresponding to each analysis. The prefix of the notebooks indicates the order in which it is run, which also corresponds to the Results sections of the manuscript. For detailed information about each notebook, see the README inside the notebooks directory.

Data

Datasets are publically available and can be directly downloaded from . The files should be unzipped and placed in the data directory.

Furthermore, the directory data contains all the figures of the manuscript (generated by the notebooks) as well as the raw and intermediary files (also generated by the notebooks).