Nested Association Mapping
SNP heritability
SNP Quality Control
Genome-wide prediction
Fixation Index
Bayesian Mixed Model
Genomic mixed model
Empirical Bayes Genome Wide Association Mapping
Internal functions
Manhattan plot for Association Studies
Nested Association Mapping
Pseudo-Expectation Gauss-Seidel for Multivariate Models
Restricted Maximum Likelihood
Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.