Accurate sample inference from amplicon data with single nucleotide resolution

Genomic Data Retrieval with R

R package for microbiome biomarker discovery

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

MaAsLin2: Microbiome Multivariate Association with Linear Models

Make Picrust2 Output Analysis and Visualization Easier

Compare different differential abundance and expression methods

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

The is mostly a wrapper tool using phyloseq and microbiome R packages.

Interactive tools for metagenome visualization and binning in R

Differential analysis of multi-omics data based on the Tweedie distribution

A comprehensive and customizable R package for microbiome analysis.

Metagenomics calibration R package

METAgenomic LONgitudinal Differential Abundance method

SHAMAN is a SHiny application for Metagenomic ANalysis including a bioinformatic workflow, the statistical analysis and multiple visualization.

Repository for all Ocean Sampling Day related source code with information on how-to acquire OSD data

Bioinformatics Pipeline

An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles

zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics

Interactive visualisation and data annotation for meta-omics data