Software

A Likelihood Approach for Mediation Analysis in Case-Control Studies

MediationCC is a set of R functions to perform mediation analyses in case-control studies using a unified likelihood framework. Our approach estimates (on the odds-ratio scale) the direct effect an exposure has on disease as well as the indirect effect the exposure has on disease through a mediator. Our software can handle either a binary or continuous mediator, as well as a continuous or binary exposure. Our method also allows for incorporation of mediator-exposure interaction effects on disease risk and can adjust for covariates of interest.

Gene Association with Multiple Traits

GAMuT consists of a set of R routines for gene-based association testing of rare polymorphic variants with multiple phenotypes. The software implements statistical methodology published in Broadaway et al. (2016).

Case-control haplotype inference package

Chaplin is software for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study. The program utilizes statistical methodology initially developed in Epstein and Satten (2003) and explored further in Satten and Epstein (2004).

Permutation procedure to correct for confounders in case-control studies

This R package is a modified version of the 'BiasedUrn' package developed by Agner Fog; the original package can be found on the CRAN site. We created this modified package to facilitate permutation-based testing of disease-exposure association in case-control studies that accounts for potential confounders. In particular, such permutation-based procedures can be used to adjust for confounders in case-control studies of rare genetic variation.

A Powerful and Flexible Multilocus Association Test for Quantitative Traits

LSKM consists of a R routine that allow for semiparametric association testing of quantitative traits with multiple SNP predictors, adjusting for environmental covariates. The software implements statistical methodology recently developed in Kwee et al. (2008). The downloaded zipped file will contain the R routine, documentation, and example input files.

Robust Joint Tests of SNP and SNP_Environment Interaction

We developed a function to allow users to perform robust joint testing of SNP and SNP-environment interaction within the PLINK software toolset for whole genome association analysis. The function was written using the R programming language. The software implements statistical methodology published in Almli et al. (2014).

Association analysis of triads and unrelated subjects

Scout is a software program for conducting combined association analysis of triads and unrelated subjects. The software utilizes statistical methodology developed in Epstein et al. (2005).

SNP-Set Kernel Association Test

SKAT consists of R routines that extend the LSKM program to handle case-control data. The software implements statistical methodology developed in Wu et al. (2010). Wu et al. (2010).

Software that controls for population stratification in case-control association studies

StratScore is a software package for genetic association mapping of disease that corrects for the confounding effects of population stratification. The software is based on a variation of the methods described in the paper of Epstein et al. (2007). Please refer to this paper for a description of the underlying statistical methods.