TUANZIDING/medical-paper-pipeline ? reverse-engineered prompt

Build me a Python tool for medical research papers that takes messy clinical data and helps turn it into a submission ready manuscript.

I want it to walk me through the full process for a retrospective observational study, starting with checking the dataset, cleaning obvious problems, handling missing values, making basic stats, and generating the main figures and tables. Then it should draft a structured paper in IMRaD format, verify references by DOI when possible, and format everything for a journal like Injury, BMJ, JAMA, or The Lancet.

It would also be great if it can generate a cover letter, a reviewer response letter, and track revisions across rounds so I can keep editing without losing work. Make it feel practical for a clinician, with clear checkpoint steps and saved progress so I can stop and resume later.

Use the README and current docs as the source of truth, and look up current online docs if you need to confirm journal formatting details.