microbial-communities topic
metaGEM
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
microbiomeutilities
The is mostly a wrapper tool using phyloseq and microbiome R packages.
MicEco
Various functions for analysis of microbial community data
melonnpan
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
smetana
SMETANA: a tool to analyse interactions in microbial communities
MEWpy
Metabolic Engineering Workbench