Quanto - Sample size and power calculations for genetic-epidemiology studies
GxEscan - Detect GxE interactions in a genome-wide association study
GxGscan - Detect GxG interactions in a genome-wide association study
PriorityPruner - PriorityPruner is a software program which can prune a list of SNPs that are in high linkage disequilibrium (LD) with other SNPs in the list, while preferentially keeping/selecting SNPs of higher priority (e.g., the most significant SNPs in a genome-wide association study).
Snagger - Snagger, as an extension to the existing open-source software, Haploview, which uses pairwise r2 linkage disequilibrium between single nucleotide polymorphisms (SNPs) to select tagSNPs.
rAggr - rAggr finds proxy markers (SNPs and indels) that are in linkage-disequilibrium (LD) with a set of queried markers, using the 1000 Genomes Project and HapMap genotype databases.
R Packagesfdrci - Permutation-based FDR Point and Confidence Interval Estimation
cit - Causal Inference Test
BVS - Bayesian Variant Selection