bacon

The software tool "bacon" addresses significant inflation and bias issues in epigenome- and transcriptome-wide association studies (EWAS and TWAS), which can lead to spurious findings if not adequately addressed. Existing methodologies and confounder adjustment methods from genome-wide association studies (GWAS) are insufficient in removing this bias and inflation. To tackle this challenge, "bacon" proposes a Bayesian approach that controls bias and inflation by estimating the empirical null distribution. The tool maximizes power through simulations and real data analysis while effectively controlling the false positive rate.