Table 2.

List of software packages for Mendelian randomization (MR) and related methods discussed in this review (this is not a comprehensive list of all MR methods but covers the methods most commonly used in the literature)

Approach	Package name	Weblink
Multiple methods	MendelianRandomization	https://cran.r-project.org/web/packages/MendelianRandomization/
Multiple methods	TwoSampleMR	https://github.com/MRCIEU/TwoSampleMR
Outlier-robust estimation	MR-PRESSO	https://github.com/rondolab/MR-PRESSO
Colocalization	coloc	https://github.com/chr1swallace/coloc
Rare variant burden testing	SKAT	https://cran.r-project.org/web/packages/SKAT/
Rare variant burden testing	regenie	https://rgcgithub.github.io/regenie/
Robust estimation for multivariable MR	Robust MVMR	https://github.com/aj-grant/robust-mvmr
Variable selection	MR-BMA	https://github.com/verena-zuber/demo_AMD
Factor-based cis-MR	con-cis-MR	https://github.com/ash-res/con-cis-MR
Network cis-MR	TwoStepCisMR	https://github.com/bar-woolf/TwoStepCisMR/wiki
Clustering variants based on outcome associations	MRClust	https://github.com/cnfoley/mrclust
Clustering variants based on trait associations	NAvMix	https://github.com/aj-grant/navmix
Non-linear residual method (individual-level data)	nlmr	https://github.com/jrs95/nlmr
Non-linear residual and doubly ranked methods	SUMnlmr	https://github.com/amymariemason/SUMnlmr
Non-linear polynomial method	PolyMR	https://github.com/JonSulc/PolyMR