microbiome R package

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

🦠 A comprehensive R package for deep mining microbiome

Qiita - A multi-omics databasing effort

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

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

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.

Various functions for analysis of microbial community data

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

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

topological data analysis of population-scale microbiomes

Analyses in R and Python Using curatedMetagenomicData

A comprehensive and customizable R package for microbiome analysis.

A Collection of Bioinformatics Projects

Metagenomics calibration R package

Tools for phylogenetic data analysis including visualization and cluster-computing support.

Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations

iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline

accessory functions for processing microbial community data