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

SMETANA: a tool to analyse interactions in microbial communities

Various functions for analysis of microbial community data

Metabolic Engineering Workbench

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

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

Functions to manipulate and visualize microbial community data

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

Minimal Supplying Community Search with constraint-based optimization methods.

Supplementary data for co-occurrence manuscript

FLYCOP (FLexible sYnthetic Consortium OPtimization)

RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.

NOTE: The iroki command line tool is no longer maintained. Please see: https://github.com/mooreryan/iroki

Higher-Order Co-occurrence

Environmental metagenomics, Spring 2021, Physalia Courses

Environmental metagenomics, Spring 2022, Physalia Courses

2017 September Microbial Community Analysis Workshop

Modelling and Inference of MICrobiomes Project (MIMIC) is a Python package dedicated to simulate, model, and predict microbial communities interactions

3D Analysis of confocal images of microbial biofilms/communities

Designing microbial communities