The R package multiMiR is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs.
EMMAX is a statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model.
LBL (Logistic Bayesian Lasso) is an R package that performs Logistic Bayesian Lasso for finding association of SNP haplotypes with a trait in a case-control setting. Bayesian lasso is used to find the posterior distributions of logistic regression coefficients, which are then used to calculate Bayes Factor to test for association with haplotypes.
LBLGXE expands on the original LBL. Gene-environment interaction (GXE)
PC-select calculates GWAS association statistics using a data-adaptive GRM that improves power over standard mixed models while simultaneously avoiding confounding from population stratification.
GWiS (a novel Gene-Wide Significance) test uses greedy Bayesian model selection to identify the independent effects within a gene, which are combined to generate a stronger statistical signal.
GENIE (previously PEDGENIE and HAPMC) performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests