Table 2. Summary of selected software packages for performing MR analyses.

Package name	Software	Description
Individual-level data
AER	R	Includes the ivreg function for two-stage least squares (2SLS) estimation
OneSampleMR	R	Various functions for one-sample instrumental variable (IV) analyses, including the Sanderson-Windmeijer F-statistic, and various estimators (two-stage predictor substitution, two-stage residual inclusion, structural mean models)
ivmodel	R	Various functions for individual level IV analyses, includes limited information maximum likelihood (LIML), weak instrument tests and sensitivity analyses.
ivtools	R	Various functions for individual level IV analyses, including functions to fit structural mean models
ivonesamplemr	Stata	Includes various estimators (two-stage predictor substitution, two-stage residual inclusion, structural mean models) for one-sample IV analyses.
ivreg2	Stata	Stata module for extended instrumental variables/2SLS and generalized method of moments (GMM) [Au:Added abbreviation - OK?YES] estimation.
ivregress	Stata	Linear IV estimators including two-stage least squares.
Summary-level data
MendelianRandomization	R	Implements several methods for performing Mendelian randomization analyses with summarized data and an interface with the PhenoScanner database.
TwoSampleMR and MR-Base app	R/web-app	MR-base is an analytical platform for Mendelian randomization. TwoSampleMR is the R package providing the functions to perform MR estimation. Both are linked to the OpenGWAS project, a large database of GWAS summary statistics.
mrrobust	Stata	Provides various programs for two-sample MR analyses in Stata