HapFABIA (Factor Analysis for Bicluster Acquisition) is an R package for identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data.
famRvTest is an efficient C++ tool for rare variant association analysis using a linear-mixed model approach. It handles population structure, familial relatedness and study-specific covariates. The tool supports both single variant and gene-level associations with various methods implemented. It has been used in eQTL and quantitative traits association analyses in T2Dgenes project.
ARR (adaptive ridge regression) is an R package to detect rare variants associated with a quantitative trait using the adaptive ridge regression method.
RWAS (Rare variant Weighted Aggregate Statistic) is a groupwise association test for identifying associations of groups of rare variants. RWAS groups variants and computes a weighted sum of differences in mutation counts between case and control individuals. Weights of RWAS are estimated from data to achieve nearly optimal power under a disease model in which all variants make an equally small contribution to population disease risk.
LRT (Likelihood Ratio Test) is a method that tries to identify which variants are causal by taking advantage of both prior information (of how likely each variant is functional) and data. LRT uses this information (of which variants are likely causal) to better detect associations of groups of rare variants.
Jae Hoon Sul, Buhm Han, Eleazar Eskin.
“Increasing Power of Groupwise Association Test with Likelihood Ratio Test.”
In Proceedings of the Fifteenth Annual Conference on Research in Computational Biology (RECOMB-2011). Vancouver, Canada: March 28th-31st, 2011
ARIEL (Accumulation of Rare variants Integrated and Extended Locus-specific test) explores the effects of rare variants within complex traits through locus-based analysis.
