Reproducibility Checklist

# Reproducibility Checklist — Open Science Best Practices

## Overview
Ensure research is reproducible, transparent, and meets open science standards.

## Pre-Registration
- [ ] Study registered on ClinicalTrials.gov, OSF, or AsPredicted before data collection
- [ ] Primary outcome and analysis plan pre-specified
- [ ] Deviations from pre-registration documented and justified

## Data Availability
- [ ] Raw data deposited in domain repository (GEO, PDB, PRIDE, Zenodo, Dryad, Figshare)
- [ ] Data dictionary/codebook provided
- [ ] Sensitive data: de-identification method documented, access controls described
- [ ] DOI assigned to dataset

## Code Availability
- [ ] Analysis code in public repository (GitHub, GitLab, Zenodo)
- [ ] Environment specification (requirements.txt, conda env, Docker, renv.lock)
- [ ] Random seeds fixed and documented
- [ ] README with reproduction instructions

## Materials
- [ ] Reagent catalog numbers, lot numbers, manufacturer
- [ ] Custom materials: synthesis protocol or request process
- [ ] Cell lines: STR authentication, mycoplasma testing
- [ ] Antibodies: RRID or Antibody Registry ID

## Statistical Reporting
- [ ] All statistical tests, parameters, and software versions reported
- [ ] Effect sizes and confidence intervals (not just p-values)
- [ ] Multiple comparison correction method stated
- [ ] Sample size justification (power analysis)

## Reporting Standards
- [ ] Applicable guideline followed (STROBE/CONSORT/PRISMA/ARRIVE/MIQE)
- [ ] Checklist completed and submitted with manuscript