Title: 'MicroRNA' Set Enrichment Analysis
Description: The tools for 'MicroRNA Set Enrichment Analysis' can identify risk pathways(or prior gene sets) regulated by microRNA set in the context of microRNA expression data. (1) This package constructs a correlation profile of microRNA and pathways by the hypergeometric statistic test. The gene sets of pathways derived from the three public databases (Kyoto Encyclopedia of Genes and Genomes ('KEGG'); 'Reactome'; 'Biocarta') and the target gene sets of microRNA are provided by four databases('TarBaseV6.0'; 'mir2Disease'; 'miRecords'; 'miRTarBase';). (2) This package can quantify the change of correlation between microRNA for each pathway(or prior gene set) based on a microRNA expression data with cases and controls. (3) This package uses the weighted Kolmogorov-Smirnov statistic to calculate an enrichment score (ES) of a microRNA set that co-regulate to a pathway , which reflects the degree to which a given pathway is associated with the specific phenotype. (4) This package can provide the visualization of the results.

Title: Microbiome Based Sum of Powered Score (MiSPU) Tests
Description: There is an increasing interest in investigating how the compositions of microbial communities are associated with human health and disease. In this package, we present a novel global testing method called aMiSPU, that is highly adaptive and thus high powered across various scenarios, alleviating the issue with the choice of a phylogenetic distance. Our simulations and real data analysis demonstrated that aMiSPU test was often more powerful than several competing methods while correctly controlling type I error rates.
Depends: R (>= 3.2.3), vegan, ape, aSPU,cluster

Title: Mixed effects Score Test for continuous outcomes
Author: Jianping Sun, Yingye Zheng, and Li Hsu
Description: Test for association between a set of SNPS/genes and
continuous or binary outcomes by including variant
characteristic information and using (weighted) score

Description: The package performs continuous-time microsimulation for population projections.
Depends: R (>= 3.0.1), chron, snowfall, rlecuyer