Software

Microbiome Host Trait Prediction Explorer

Visualization Tool for Imputation and Prediction of Biomedical data

ZIBBSeqDiscovery – Zero Inflated Beta-Binomial Modeling of Microbiome Count data

MCC – Moment Corrected Correlation Method on High Dimensional Data

PCFAM - Computation of Ancestry Scores with Mixed Families and Unrelated Individuals 

PathwaySeq - Pathway Analysis for RNA-Seq Data (You need R 3.1.1) 

BBSeq – Analysis of RNA-seq count data.

quad - Exact Permutation Moments of Quadratic Form Statistics

SafeExpress - Empirical Pathway Analysis, without Permutation 

Tutorial of  Machine Learning Methods for Microbiome Host Trait Prediction (open the readme file first)

CorDiff- Set-based Differential Covariance Testing for Genomics (R package )   Real data

A Note on Cyclic Shift Permutation Testing for Large Eigenvalues (R code, data)

Simultaneous modeling of multivariate heterogeneous responses and heteroskedasticity via a two-stage composite likelihood (R code)