Versatile open-source tool for microbiome analysis

Using R language in microbiome analysis

An R package for downstream data analysis of microbiome omics data

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

Orchestrating Microbiome Analysis

Vanilla regression methods for microbiome differential abundance analysis

Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM function.

R shiny app for interactive microbiome analysis

Microbiome analysis

A fast and scalable phylogenetic tree viewer for microbiome data analysis

MGM (Microbial General Model) as a large-scaled pretrained language model for interpretable microbiome data analysis.

The EasyMultiProfiler package aims to offer a user-friendly and efficient multi-omics data analysis tool on the R platform. It facilitates various essential tasks related to microbiome, genome, and metabolite downstream analysis, providing a seamless workflow from start to finish.

For analysis of microbiome and microbial community data

A Python package for microbiome sequencing analysis with QIIME 2

Pipeline & Reproducible analysis examples for amplicon and metagenome in microbiome

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers

Ying's tools for analysis, with particular focus on microbiome data

:microbe: A shiny package for microbiome functional enrichment analysis

Analysis framework for integrating gut microbiome and host gene expression data

An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studies using random effects models

Archive: Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction". Please check our ANCOMBC R package for the most up-to-date ANCOM-BC function.

topological data analysis of population-scale microbiomes

Rice (Oryza Sative) root microbiome time-course analysis. (Zhang2018SCLS)

R package for downstream Microbiome analysis

Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL

Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.

Bayesian Inferential Regression for Differential Microbiome Analysis

R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.

A microbiome analysis toolkit for R