Microbiome Python Packages

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

micom

Microbial community modeling based on cobrapy.

dram-bio

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

miscoto

Python package for large-scale community selection in microbiota

micone

The Microbial Co-occurrence Network Explorer

emperor

Emperor

redbiom

Sample search by metadata and features

singlem

Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes

microberx

MicrobeRX

amptk

AMPtk: amplicon tool kit

amon-bio

Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data

woltka

versatile meta-omic data classifier

qurro

Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

dbbact-calour

dbBact (https://dbbact.org) interface for Calour (https://github.com/biocore/calour) for microbiome 16S analysis

microbiome-toolbox

Early Life Microbiome Toolbox

superfocus

SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data

empress

Fast and scalable phylogenetic tree viewer for multi-omic data analysis

pymgpipe

Python implementation of mgpipe

metagenomics-focus

FOCUS: An Agile Profiler for Metagenomic Data

mitre

The Microbiome Interpretable Temporal Rule Engine

mibiscreen

Prediction tool for Microbiome based Remediation

qiime-tools

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

tmarsel

Repository for TMarSel

compositional

Python package for compositional data analysis including CLR/ILR, proportionality, partial correlation with basis shrinkage, and visualizations.