Our group has developed several tools for the analysis of genetics and genomics datasets. These tools and webservers which display the results of analysis with these tools are available to the scientific community.
CAVIAR CAVIAR (CAusal Variants Identication in Associated Regions), a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants.
EMMAX Efficient Mixed Model Association eXpedited - A method for correction of population structure in genome wide association studies.
RAREVARIANTS Software for association studies over rare variants.
POWERDESIGN Webserver for generating genetic association study designs which maximize statistical power.
WHAP Weighted HAPlotype association server which increases power of association studies by leveraging linkage disequilibrium patterns estimated from the HapMap.
HAP Haplotype Resolution using Imperfect Phylogeny to recover haplotypes from genotype data. Resolve genotypes using our webserver.
SPA Spatial Ancestry analysis (SPA) is a method for predicting ancestry or where an individual is from using the individual's DNA. Accurately modeling ancestry is an important step in identifying genetic variation involved in disease.
NICE Next-generation Intersample Correlation Emended (NICE) is a statistical test for correcting for expression heterogeneity inherent in expression dataset due to confounding from unmodeled factors. NICE estimates inter-sample correlation structure using only the genes with confounding effects and incorporates it as signatures of the systematic confounding effects to correct for it.
METASOFT/ForestPMPlot METASOFT is a free, open-source meta-analysis software tool for genome-wide association study analysis, designed to perform a range of basic and advanced meta-analytic methods in an efficient manner. ForestPMPlot is a free, open-source a python-interfaced R package tool for analyzing the heterogeneous studies in meta-analysis by visualizing the effect size differences between studies. The resulting plot can facilitate the better understanding of heterogeneous genetic effects on the phenotype in different study conditions.
GRAT Genome-wide Rapid Association Testing
SLIP and SLIDE SLIDE (Sliding-window method for Locally Inter-correlated markers with asymptotic Distribution Errors corrected) is a multivariate normal distribution (MVN)-based multiple hypothesis testing correction method. SLIDE shows a near identical accuracy to the gold standard, the permutation test, and is much faster. SLIP (Sliding-window method for Locally Inter-correlated markers for Power estimation) is a multivariate normal distribution (MVN)-based power estimation method. SLIP shows a near identical accuracy to the standard simulation procedure for power, and is much faster.
GraphIBD is a free, open-source IBD association testing software for genome-wide association study analysis.
TEPAA is a strategy to reduce the number of SNP pairs needed for epistasis detection while maintaing similar power with brute force approach. We use TEPAA to compute which SNP pair should be checked to see whether the p-value is significant. The p-value is computed by other software package, such as Pylmm and EMMAX.
CNVem aims to detect copy number variations (CNVs) using HTS reads. We especially pay attention to the reads that map to multiple locations.
HARSH HAplotype inference using Reference and Sequencing tecHnology (HARSH) is a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. It is based on a novel probabilistic model and Gibbs sampler method.
PyLMM A fast and lightweight python-based linear mixed-model solver for use in genome-wide association studies.
MultiTrans Multiple testing in transformed space.
GAMMA Generalized Analysis of Molecular variance for Mixed model Analysis.
EMMA Efficient Mixed Model Association - A method for correction of population structure in model organism association studies.
EMMA Study Design Model Organism Association Study Design. Software package for calculating power of model organism association study designs.
MPAD Mouse Phenome Association Database. Genome browser displaying associations between common inbred strains and JAX Labs Mouse Pheome Database phenotypes.
MITRA MIsmatch TRee Aproach to discovering regulatory elements in DNA sequences. Find Motifs using MITRA on our webserver.
VGA Viral Genome Assembler (VGA) is a method for accurate assembly of a heterogeneous viral population consisting of individuals viral genomes (also known as quasi-species). VGA is coupled with a high-fidelity sequencing protocol able to eliminate errors from sequencing data.
This website is supported by National Science Foundation grants 0513612, 0731455, 0729049, 0916676, 1065276, 1302448 and 1320589, and National Institutes of Health grants K25-HL080079, U01-DA024417, P01-HL30568, P01-HL28481, R01-GM083198, R01-ES021801, R01-MH101782 and R01-ES022282.