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

deeptaxa-rrna

Hybrid CNN-BERT deep learning for hierarchical taxonomic classification of 16S rRNA sequences

miscoto

Python package for large-scale community selection in microbiota

emperor

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

singlem

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

microberx

MicrobeRX is A tool for enzymatic reaction-based metabolite prediction in the gut microbiome.

mibiscreen

Prediction tool for Microbiome based Remediation

vgi-scikit-bio

scikit-bio for DuckDB/SQL — sequence analysis, pairwise alignment, community diversity, ordination, and phylogenetics, exposed as a VGI worker

amon-bio

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

amptk

AMPtk: amplicon tool kit

micone

The Microbial Co-occurrence Network Explorer

dbbact-calour

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

compositional

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

redbiom

Sample search by metadata and features

microbiome-toolbox

Early Life Microbiome Toolbox

famli

Functional Analysis of Metagenomes by Likelihood Inference

qurro

Visualizes differentially ranked features and log-ratios of their sample abundances

empress

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

woltka

Woltka: a versatile meta'omic data classifier

superfocus

A tool for agile functional analysis of shotgun metagenomic data

mitre

Microbiome Interpretable Temporal Rule Engine

metagenomics-focus

FOCUS: An Agile Profiler for Metagenomic Data