Using real genotype data, simulate a complex trait as a function of latent expression, fit eQTL weights in independent data, and perform GWAS/TWAS on complex trait.

TWAS-pipeline

PhenoPLIER

Tool for integrative gene-based association analysis using GWAS summary stats

Epigenomewide Association Studies (EWAS) with FUnctional Summary-based ImputatiON (FUSION)

Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits

Summary-level Unified Method for Modeling Integrated Transcriptome

Optimizing transcriptome prediction models for use in multi-ethnic TWAS using multivariate adaptive shrinkage.

Analysis of transcriptome imputation using paired genotype-expression data from SAGE and GEUVADIS

A Haplotype-Resolved Transcriptome-Wide Association Framework.

tool for continuously integrated meta-resource

LocusXcanR: an R package that creates an R Shiny application that aids TWAS interpretation, can be extended to other ‘omics data, and highlights R Shiny’s effectiveness at presenting results in an approachable, interactive, and visual format.

bsBSLMM: a block-sparse extension of BSLMM with annotation-informed per-SNP priors for cis-expression prediction

client to the cimr-d database for continuous integration and analysis using cimr

End-to-end TWAS pipeline for Alzheimer's disease integrating Kunkle et al. (2019) GWAS summary statistics with GTEx v8 MASHR brain eQTL models to identify causal genes via cross-tissue omnibus regression and functional pathway over-representation analysis.

RAISING: Automated deep learning framework

Bioinformatic software to identify causal variants in GWAS and GWAS/eQTL studies.

Code to generate the data and website for Rat TWAS Hub

Factored QTL analysis applied to GTEx and GWAS of 114 complex traits