MicrobiomeR
MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows - Published in JOSS (2019)
microViz
microViz: an R package for microbiome data visualization and statistics - Published in JOSS (2021)
Tidytacos
Tidytacos: An R package for analyses on taxonomic composition of microbial communities - Published in JOSS (2025)
MicrobiotaProcess
:microbe: A comprehensive R package for deep mining microbiome
omeinfo
Automated retrieval of consistent geographical metadata for microbiome research!
phylotoast
Tools for phylogenetic data analysis including visualization and cluster-computing support.
https://github.com/erictleung/dada2hpcpipe
:ocean: 16S rRNA microbiome data analysis workflow using DADA2 and R on a high performance cluster using SLURM
https://github.com/ahmedmoustafa/als
Analysis of the gut microbiome of Amyotrophic Lateral Sclerosis (ALS) patients using the DADA2 workflow
https://github.com/almaaslab/micint
R package for analyzing microbial co-occurences
https://github.com/cafferychen777/microbiomestat-turtorial-professional-version
MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.
https://github.com/cafferychen777/microbiomestat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
https://github.com/cafferychen777/microbiomestat-shiny
A Shiny interface for the MicrobiomeStat R package, designed to facilitate analysis and visualization of microbiome data.