equity-scorer

What problem does it solve?

Measure how well a genomic dataset represents global population diversity and detect underrepresentation that can bias downstream analyses, by turning genotype or ancestry files into interpretable equity metrics and visualisations.

Core Features & Use Cases

• Heterozygosity Analysis: Compute observed and expected heterozygosity per population to assess within-group genetic diversity.
• Population Differentiation: Calculate pairwise FST and render heatmaps to quantify between-population structure.
• Dimensionality Reduction & Visuals: Run PCA and produce publication-ready PCA plots, ancestry distribution bars, heterozygosity comparisons, and a HEIM gauge.
• Composite HEIM Equity Score & Reports: Produce a 0-100 HEIM Equity Score with a reproducible markdown report, figures, CSV tables, and checksums for reproducibility.
• Use Cases: Evaluate biobank representativeness, compare cohort recruitment strategies, QC cohort ancestry composition before association analyses.

Quick Start

Run the equity-scorer on a VCF or ancestry CSV to compute heterozygosity, pairwise FST, PCA plots, and a HEIM Equity Score with a reproducible markdown report.