andyzhuang/skills/labclaw/general/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