FOCUS (Fine-mapping Of CaUsal gene Sets) is software to fine-map transcriptome-wide association study statistics at genomic risk regions. The software takes as input summary GWAS data along with eQTL weights and outputs a credible set of genes to explain observed genomic risk.
TWAS Simulator is software to simulate a complex trait as a function of latent steady-state expression, fit eQTL weights in independent data, and perform GWAS+TWAS on the simulated complex trait.
FIZI (Functionally-Informed Z-score Imputation) leverages functional information together with reference linkage-disequilibrium (LD) to impute GWAS summary statistics (Z-scores).
RHOGE is an R package that estimates the genome-wide genetic correlation between two complex traits (diseases) as a function of predicted gene expression effect on trait (ρge). Given output from two transcriptome-wide association studies, RHOGE estimates the mediating effect of predicted gene expression and estimates the correlation of effect sizes across traits (diseases). This approach is extended to a bi-directional regression that provides putative causal directions between traits with non-zero ρge.