Software

MPAT is an R package for performing multiple phenotype association tests based on univarite GWAS summary statistics. It provides a toolkit of testing procedures to aggregate association evidence across multiple phenotypes for a given genetic variant. All the p-alues can be efficiently computed. It can be downloaded at:  MPAT and its user manual is at: Manual 

DACT is an R package for testing for the mediation effects in genome-wide epigenetic studies. It can be downloaded at:  DACT 

MICS is an R packae for testing cell-type specific mediation effects in genome-wide epigenetic studies. It can be downloaded at: MICS

MRCIP ia an R package for the inference of causal relationship between traits based on summary-level GWAS data, which accounts for the correlated pleiotropy and idiosyncratic pleiotropy. It can be downloaded at: MRCIP 

ERstruct is a MATLAB toolbox for inferring the number of top principal components from whole genome sequencing data. It can be downloaded at:  ERStruct  and the python version is available at: ERStruct .

MRMiSTERI is an R package for performing robust Mendelian randomization with invalid IVs using individual level data. It can be downloaded at: MRMiSTERI 

RBMR is an R package for performing the robust two-sample Bayesian mendelian randomization while accorting for the linkage disequilibrium and idiosyncratic pleiotropy at: RBMR 

omniTest  is an R package for performing robust multiple traits analysis based on GWAS summary statistics. It can be downloaded at:omniTest 

EBMMT is an R package to test for the associations between a genetic variant and multiple traits based on GWAS summary statistics. It can be downloaded at: EBMMT 

pIVW is an R package for the penalized inverse-variance weighted (pIVW) estimator is a Mendelian randomization method for estimating the causal effect of an exposure variable on an outcome of interest based on summary-level GWAS data while accounting for the weak instruments and horizontal pleiotropy. It is available at: pIVW.

 ImmuneMirror  is a web application that helps to identify the key genomic and transcriptomic features associated with response of cancer immunotherapy. 

 DeepMed is an R package  for estimating the natural (in)direct effects of a binary treatment on an outcome of interest in the semi-parametric causal mediation analysis framework using deep neural networks.

MRSquared is an R package for performing robust Mendelian randomization methods with invalid IVs using interaction IVs. It is available at https://github.com/zhonghualiu/MRSquared.