Table 2.

Programs and software for power calculations and analysis

Program/Macro	Specific Uses	Website	Reference
SAS macro GEmis2	Power calculations Addresses misclassification in E	http://www.hsph.harvard.edu/faculty/peter-kraft/software/	[Lindstrom, et al. 2009]
Quanto	Power calculations GxE and joint test, case-control, case-only, family-based designs, continuous outcome	http://biostats.usc.edu/software	[Gauderman 2002a; Gauderman 2002b]
Power	Power calculations Additive Interactions	http://dceg.cancer.gov/tools/design/POWER	[García-Closas and Lubin 1999]
Stata program	Power calculations GxE test from logistic regression	http://ideas.repec.org/p/boc/asug03/07.html	[Katie, et al. 2003]
PLINK	Analysis for discovery GEWIS data handling, GE test, joint test	http://pngu.mgh.harvard.edu/~purcell/plink/	[Purcell, et al. 2007]
ProbABEL	Analysis for discovery GEWIS computes robust variance-covariance matrix	http://www.genabel.org/packages/ProbABEL	[Aulchenko, et al. 2010]
GxEscan	Analysis for discovery GEWIS Implements a suite of testing methods for GEWIS data, including efficient 2-step methods	http://biostats.usc.edu/software	[Gauderman, et al. 2013a]
Multassoc	Analysis for discovery and characterization Test a group of SNPs taking interaction with other G, E into account	http://dceg.cancer.gov/tools/analysis/multassoc	[Chatterjee, et al. 2006]
METAL	Meta-analysis Common package for combining existing GWAS results	http://genome.sph.umich.edu/wiki/Meta_Analysis_of_SNPxEnvironment_Interaction	[Willer, et al. 2010]
CGEN	Analysis for discovery and characterization R package implementing a suite of testing and estimation methods for GxE studies	http://bioconductor.org/packages/release/bioc/html/CGEN.html	[Bhattacharjee, et al. 2012]