Microbiome Data Analysis & Meta-Analysis with GAMLSS-BEZI & Random Effects
Compare multiple alpha diversity indexes between groups
Nice meta-analysis plots.
Meta-analysis of taxa/pathway abundance comparison.
Display meta-analysis results.
Predict microbiome age.
Compare (kegg) pathway abundance
Read multiple files
Compare taxa relative abundance
Filter relative abundance data
Plot mean taxa abundance
Summarize abundance by group
Display abundance comparison results.
Generalized Additive Model for Location, Scale and Shape (GAMLSS) with zero inflated beta (BEZI) family for analysis of microbiome relative abundance data (with various options for data transformation/normalization to address compositional effects) and random effects meta-analysis models for meta-analysis pooling estimates across microbiome studies are implemented. Random Forest model to predict microbiome age based on relative abundances of shared bacterial genera with the Bangladesh data (Subramanian et al 2014), comparison of multiple diversity indexes using linear/linear mixed effect models and some data display/visualization are also implemented. The reference paper is published by Ho NT, Li F, Wang S, Kuhn L (2019) <doi:10.1186/s12859-019-2744-2> .
Useful links