Microbiome Python Packages

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

micom

Python package to study microbial communities using metabolic modeling.

dram-bio

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

miscoto

Microbiome Screening and COmmunity selection using TOpology

singlem

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

emperor

Emperor a tool for the analysis and visualization of large microbial ecology datasets

microberx

MicrobeRX

amon-bio

Annotation of Metabolite Origin via Networks: A tool for predicting putative

amptk

AMPtk: amplicon tool kit

redbiom

Sample search by metadata and features

micone

The Microbial Co-occurrence Network Explorer

woltka

versatile meta-omic data classifier

compositional

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

dbbact-calour

dbbact-calour is a Calour (https://github.com/biocore/calour) interface for dbBact (dbbact.org)

qurro

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

microbiome-toolbox

Microbiome Toolbox

empress

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

superfocus

A tool for agile functional analysis of shotgun metagenomic data

famli

Functional Analysis of Metagenomes by Likelihood Inference

tmarsel

Repository for TMarSel

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