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

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

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

Minimal Supplying Community Search with constraint-based optimization methods.

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

Supplementary data for co-occurrence manuscript

NOTE: The iroki command line tool is no longer maintained.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

FLYCOP (FLexible sYnthetic Consortium OPtimization)

Higher-Order Co-occurrence

Functions to manipulate and visualize microbial community data

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

Environmental metagenomics, Spring 2021, 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

Environmental metagenomics, Spring 2022, Physalia Courses

3D Analysis of confocal images of microbial biofilms/communities

Designing microbial communities