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
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.