Bioinformatics Pipeline Validation (ICC, Cohen's Kappa, Spearman)
I validate bioinformatics pipelines by comparing their outputs with reference results using reliability metrics rather than accuracy alone: ICC for continuous measurements, Cohen's Kappa for categorical agreement and Spearman for rank correlation. Acceptance thresholds are written into a specification before building, and the whole validation is documented so it can be reproduced and reviewed.
Book a discovery callWho is it for?
- Genomics, transcriptomics and epigenomics teams moving a pipeline to production
- Biotech and pharma groups that need audit-ready evidence
- Research units whose pipeline results must be reproducible
What you get
- Validation specification with acceptance criteria
- Reliability analysis (ICC, Kappa, Spearman) with interpretation
- Reproducible environment and execution scripts
- Validation report ready for internal or external review
How it works
- 1Define the intended use and the reference data
- 2Write the specification and thresholds
- 3Run the comparison and analyse disagreements
- 4Document and hand over a reproducible package
Typical scope and pricing
Every engagement starts with a 30-minute discovery call. Pricing is custom and depends on scope; the Discovery, Build and Scale packages describe the usual ways of working. I work from Valencia, remotely with teams across Europe and the USA, in English and Spanish.
Related case studies
Frequently asked questions
Why is accuracy not enough to validate a pipeline?
If 95% of variants are benign, a pipeline that calls everything benign reaches 95% accuracy but a Kappa of 0. Reliability metrics correct for chance agreement and give a realistic picture.
Which metric should I use?
ICC for continuous measurements, Cohen's Kappa for categorical calls and Spearman for rank agreement. The choice depends on the data type and the intended use.
Can you work with our existing pipeline?
Yes. I validate pipelines built in Nextflow, Python or R, and I document the environment so the results can be reproduced.