[Epistasis Tools]

Epistasis Tools is a collection of efficient programs for epistasis detection in genome-wide data. With user-provided genotype and phenotype data, as well as a few parameters, the programs are able to return the significant SNP-pairs. The programs are implementations of efficient epistasis detection algorithms, which greatly speed up the computationally intensive process.

Currently, the collection consists of three main programs: FastANOVA[paper], COE[paper], and TEAM[paper]. The three programs are suitable for different problem settings. Please refer to the following table for the setting that is suitable for each program.

Algorithm Genotype Phenotype Error Type Sample Size Supported Test
FastANOVA homozygous quantitative FWER less than a hundred ANOVA test
COE homozygous binary FWER less than a hundred convex tests
TEAM heterozygous binary FWER & FDR hundreds of thousands tests based on
contingency tables

Besides source code(link), we also provide a web-interface for the applications. To use the applications online, users need to follow the listed steps.

(1) Register a user name in Registration
(2) Select an application on the left panel
(3) Upload the datasets and set the parameters
(4) Click the [Submit] button
(5) Monitor the status and get the result in Progress Monitor

Please note that the size limit of the uploaded dataset is 3 Megabytes. For analysis that involves large or sensitive datasets, it is recommended to download and run the programs.