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
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
Metabolic Engineering Workbench
The is mostly a wrapper tool using phyloseq and microbiome R packages.
Minimal Supplying Community Search with constraint-based optimization methods.
Functions to manipulate and visualize microbial community data
Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models
FLYCOP (FLexible sYnthetic Consortium OPtimization)
Modelling and Inference of MICrobiomes Project (MIMIC) is a Python package dedicated to simulate, model, and predict microbial communities interactions
Supplementary data for co-occurrence manuscript
Environmental metagenomics, Spring 2021, Physalia Courses
NOTE: The iroki command line tool is no longer maintained. Please see: https://github.com/mooreryan/iroki
Designing microbial communities
Environmental metagenomics, Spring 2022, Physalia Courses
Environmental metagenomics, Spring 2023, Physalia Courses
2017 September Microbial Community Analysis Workshop
3D Analysis of confocal images of microbial biofilms/communities
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