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Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLINK, scikit-allel, and LDBlockShow. Use when calculating LD or pruning variants.
Runs cis-pQTL Mendelian randomization for drug-target validation using UKB-PPP (Olink), deCODE (SomaScan), Fenland, INTERVAL, ARIC, and FinnGen-PPP proteomes plus colocalization triangulation, phenome-wide on-target adverse-effect scans, cross-platform Olink/SomaScan replication, and PAV (protein...
Single-variant common-variant GWAS with plink2 --glm (linear/logistic, Firth) and the linear mixed models GEMMA, BOLT-LMM, SAIGE, regenie (SPA). A GWAS statistic is valid only when genotype is independent of unmodeled phenotype drivers after the chosen covariates and random effects, so the engine...
Infers and describes population structure with PCA (plink2 --pca, smartpca/EIGENSOFT, FlashPCA2), model-based clustering (ADMIXTURE, fastSTRUCTURE), FST estimators (Weir-Cockerham vs Hudson), and f-statistics (f3/f4/D via AdmixTools/admixr), plus Python plotting of PCs and Q barplots. Every outpu...
End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association
End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative traits. Use when running genome-wide association studies.
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