ancombc2

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

RAPID - R based Amplicon Pipeline for Interactive DADA2 - A unified Shiny application that takes you from raw amplicon data to ASV and taxonomy tables with DADA2, and onward to ecology visualizations, PERMANOVA, and ANCOM-BC2 analyses.

Benchmarking DESeq2, MaAsLin2, and ANCOM-BC2 on simulated microbiome data with known differential taxa.

R scripts for microbiome preprocessing, differential abundance analysis, and machine learning–based prediction of rheumatoid arthritis.