Data

Tools

Indexes

Applications

Experiments

Awesome

An open API service indexing awesome lists of open source software.

Projects in Awesome Lists tagged with microbiome

A curated list of projects in awesome lists tagged with microbiome .

https://github.com/benjjneb/dada2

Accurate sample inference from amplicon data with single nucleotide resolution

amplicon bioconductor bioinformatics metabarcoding metagenomics microbiome taxonomy

Last synced: 18 Feb 2026

https://github.com/wrightonlabcsu/dram

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

annotation bioinformatics genomics metagenome-assembled-genomes metagenomics microbiome viral-genomics viral-metagenomics

Last synced: 04 Feb 2026

https://github.com/biocore/qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

analysis microbiome

Last synced: 17 Dec 2025

https://github.com/WrightonLabCSU/DRAM

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

annotation bioinformatics genomics metagenome-assembled-genomes metagenomics microbiome viral-genomics viral-metagenomics

Last synced: 23 Mar 2025

https://github.com/franciscozorrilla/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

bioinformatics computational-biology flux-balance-analysis genome-scale-metabolic-model gut-microbiome mags metabolic-modeling metabolic-models metabolism metagenome-assembled-genomes metagenomics microbial-ecology microbiome snakemake systems-biology

Last synced: 25 Jun 2025

https://github.com/franciscozorrilla/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

bioinformatics computational-biology flux-balance-analysis genome-scale-metabolic-model gut-microbiome mags metabolic-modeling metabolic-models metabolism metagenome-assembled-genomes metagenomics microbial-ecology microbiome snakemake systems-biology

Last synced: 11 Apr 2025

https://github.com/benjjneb/decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

amplicon bioinformatics contamination metabarcoding metagenomics microbiome

Last synced: 21 Feb 2026

https://github.com/MaximilianKohler/HumanMicrobiome

Human Microbiome wiki

health microbiome science

Last synced: 01 May 2025

https://github.com/qiita-spots/qiita

Qiita - A multi-omics databasing effort

microbiome microbiome-analysis python

Last synced: 17 Dec 2025

https://github.com/frederickhuanglin/ancombc

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

ancom ancombc ancombc2 correlation differential-abundance-analysis microbiome normalization secom sequencing

Last synced: 20 Oct 2025

https://github.com/mangiolalaboratory/sccomp

Mixed-effect model to test differences in cell type proportions from single-cell data, in R

batch-correction bayesian composition cytof differential-proportion microbiome multilevel proportions r-package random-effects single-cell unwanted-variation

Last synced: 20 Oct 2025

https://github.com/pirovc/ganon

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

bioinformatics bloom-filter genbank gtdb k-mer metagenomics microbiome minimizers ncbi refseq taxonomy

Last synced: 28 Feb 2026

https://github.com/microbiome/oma

Orchestrating Microbiome Analysis

bioconductor microbiome microbiome-analysis-book r

Last synced: 16 May 2025

https://github.com/biocore/gemelli

Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.

compositional-data-analysis ctf joint-rpca microbiome qiime2 rclr rpca tempted

Last synced: 04 Apr 2025

https://github.com/qiyunzhu/woltka

Woltka: a versatile meta'omic data classifier

bioinformatics metagenomics microbiome

Last synced: 08 May 2025

https://github.com/will-rowe/hulk

Histosketching Using Little Kmers

genomics hashing microbiome sketching

Last synced: 12 Jan 2026

https://github.com/biocore/emperor

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

bioinformatics biplots emperor microbiome ordination python visualization

Last synced: 06 Apr 2025

https://github.com/biocore/empress

A fast and scalable phylogenetic tree viewer for microbiome data analysis

bioinformatics biplot microbiome ordination phylogeny qiime qiime2 tree-plot visualization

Last synced: 24 Apr 2025

https://github.com/microbiome/mia

Microbiome analysis

analysis bioconductor microbiome

Last synced: 16 May 2025

https://github.com/ecojulia/microbiome.jl

For analysis of microbiome and microbial community data

biology ecology julia-language microbiome

Last synced: 15 Oct 2025

https://github.com/biocore/redbiom

Sample search by metadata and features

bioinformatics biom microbiome qiime

Last synced: 13 May 2025

https://github.com/biobakery/melonnpan

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

biobakery bioconductor machine-learning metabolite-compounds metabolite-prediction metabolomics metagenomics microbial-communities microbiome multi-omics public tools

Last synced: 30 Oct 2025

https://github.com/microsud/microbiomeutilities

The is mostly a wrapper tool using phyloseq and microbiome R packages.

16s amplicon core-microbiome metagenomics microbial-communities microbiome microbiome-analysis qc-pipeline sequencing

Last synced: 26 Oct 2025

https://github.com/biocore/qurro

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

bioinformatics microbiome qiime visualization

Last synced: 18 Jul 2025

https://github.com/biocore/q2-qemistree

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

cheminformatics fragmentation-trees metabolomics microbiome phylogenetics

Last synced: 13 May 2025

https://github.com/biocore/calour

exploratory and interactive microbiome analyses based on heatmaps

bioinformatics exploratory heatmap jupyter-notebook microbiome

Last synced: 13 Jul 2025

https://github.com/shandley/microbiome-analysis-using-r

Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.

16s dada2 microbiome phyloseq teaching

Last synced: 23 Mar 2025

https://github.com/biocore/birdman

Bayesian Inferential Regression for Differential Microbiome Analysis

bayesian-inference bioinformatics microbiome python regression stan

Last synced: 13 May 2025

https://github.com/jolespin/compositional

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

compositional-data-analysis genomics-data microbiome

Last synced: 05 Oct 2025

https://github.com/fredhutch/famli

Functional Analysis of Metagenomes by Likelihood Inference

bioinformatics metagenomics microbiome

Last synced: 27 Jul 2025

https://github.com/biocore/qadabra

Snakemake workflow for comparison of differential abundance ranks

bioinformatics differential-abundance machine-learning metagenomics microbiome pipeline snakemake workflow

Last synced: 13 May 2025

https://github.com/ngless-toolkit/ng-meta-profiler

Profiler for metagenomics based on NGLess

bioinformatics metagenomics microbiome ngless

Last synced: 27 Oct 2025

https://github.com/pirovc/grimer

GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.

amplicon bokeh contamination dashboard interactive-visualizations metagenomics microbiome visualization

Last synced: 28 Feb 2026

https://github.com/eldeveloper/dogs

Companion notebooks for "Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks"

16s ibd jupyer microbiome notebook qiime

Last synced: 31 Aug 2025

https://github.com/microbiome/miaviz

Microbiome Analysis Plotting and Visualization

bioconductor microbiome microbiome-analysis plotting visualization

Last synced: 22 Aug 2025

https://github.com/gibsramen/qupid

Case-control matching for microbiome data

bioinformatics case-control microbiome python

Last synced: 13 May 2025

https://github.com/blekhmanlab/MicroBioMap

R package for fetching and parsing data of the Human Microbiome Compendium

bioinformatics microbiome microbiome-data rstats taxonomy

Last synced: 05 Apr 2025

https://github.com/maxibor/sourcepredict

Prediction/source tracking of metagenomic samples source using machine learning

machine-learning microbiome source-tracking

Last synced: 22 Jan 2026

https://github.com/cfrioux/miscoto

Python package for large-scale community selection in microbiota

answer-set-programming bioinformatics microbiome symbiont

Last synced: 29 Jul 2025

https://github.com/microbiome/microbiomedatasets

Experiment Hub based microbiome datasets

bioconductor experiment-hub microbiome microbiome-datasets

Last synced: 04 Jul 2025

https://github.com/dhimmel/fratjuice

Uncovering the microbes of fraternity basements

fraternity fratjuice microbiome sequencing ubiome

Last synced: 12 Apr 2025

https://github.com/erictleung/phyloseq-cheatsheet

:notebook: Minimal cheatsheet for functions in the phyloseq R package

bioconductor bioinformatics cheatsheet data-analysis microbiome microbiota notes phyloseq r

Last synced: 25 Mar 2025

https://github.com/microbialgenomics-irsicaixaorg/dar

dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.

bioconductor biomarker-discovery differential-abundance-analysis feature-selection microbiology microbiome phyloseq rstats

Last synced: 21 Feb 2026

https://github.com/erictleung/shinydiversity

Interactive application to explore various ecological diversity metrics

amplicon-sequencing diversity ecology interactive-visualizations metagenomics microbiome r shiny

Last synced: 25 Mar 2025

https://github.com/gibsramen/evident_

Effect size calculations for microbiome data

data-visualization microbiome python qiime2 statistics visualization

Last synced: 13 May 2025

https://github.com/gibsramen/xebec

Snakemake pipeline for microbiome diversity effect size benchmarking

bioinformatics microbiome pipeline snakemake

Last synced: 13 May 2025

https://github.com/microsud/chkmocks

Check your mock communities from microbiome sequencing experiments

microbiome zymobiomics

Last synced: 01 Jul 2025

https://github.com/systems-genomics-lab/deeptaxa

A deep learning framework for hierarchical taxonomy classification of 16S rRNA gene sequences

16s-rrna bert cnn convolutional-neural-networks deep-learning machine-learning microbiome python taxonomic-classification torch transformers

Last synced: 16 Aug 2025

https://github.com/biocore/dsfdr

descrete False Discovery Rate method

microbiome statistics

Last synced: 24 Jun 2025

https://github.com/erictleung/dada2hpcpipe

:ocean: 16S rRNA microbiome data analysis workflow using DADA2 and R on a high performance cluster using SLURM

16s amplicon-sequencing dada2 microbiome microbiome-analysis performance-cluster pipeline slurm workflow

Last synced: 25 Mar 2025

https://github.com/thejacksonlaboratory/mbiome_containers

Docker and Singular container definition files, as used by the MbiomeCore at JAX-GM

containers docker microbiome singularity

Last synced: 18 May 2026

https://github.com/microbiome/iseetree

extension of iSEE for TreeSE

microbiome shiny-apps visualisation

Last synced: 20 Jul 2025

https://github.com/cafferychen777/microbiomestat-turtorial-professional-version

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.

16s 16s-rrna 16s-seq analysis data-analysis metagenomes metagenomic-analysis metagenomic-pipeline metagenomics microbiome microbiome-analysis microbiome-analysis-pipelines microbiome-data microbiome-workflow omics omics-data omics-data-analysis omics-data-integration visualization

Last synced: 03 Jan 2026

https://github.com/erictleung/microbiome-analysis-resources

:microscope: Resources and notes on studying the human microbiome

bioinformatics data-analysis gut-microbiome microbiology microbiome notes resources

Last synced: 18 Jan 2026

https://github.com/wejlab/legato

An R-based Longitudinal mEtaGenomic Analysis Toolkit for microbiome data

analysis bioconductor bioinformatics longitudinal metagenomics microbiome

Last synced: 04 Jun 2026

https://github.com/multiomics-analytics-group/abaco

Batch Effect Correction framework for metagenomic data

batch-correction bioinformatics-software metagenomics microbiome python

Last synced: 31 Aug 2025

https://github.com/krisrs1128/multimedia

multimedia is an R package for multimodal mediation analysis of microbiome data. It has been designed to help integration of relative abundance, survey, and metabolomic data through causal mediation analysis.

causal-inference data-integration mediation-analysis microbiome

Last synced: 21 Feb 2026

https://github.com/cometsong/jaxid_generator

Microbiome-Core JAXid tracking ID code generator and view/search web app

django generator lims microbiome tracking web-application

Last synced: 15 May 2026

https://github.com/muellsen/mna

MATLAB scripts and functions for Microbial Network Analysis (MNA)

graphlets microbial microbiome networks

Last synced: 10 Oct 2025

https://github.com/eldeveloper/phd-thesis

Doctoral dissertation

emperor microbiome qiime

Last synced: 15 Feb 2026

https://github.com/clemente-lab/mmeds-meta

A database for storing and analyzing omics data

database microbiome microbiome-analysis microbiome-data python sql-database

Last synced: 11 Mar 2026

https://github.com/schlosslab/hannigan_conjunctisviribus_ploscompbio_2018

Using graph database techniques to understand the infectious relationships between bacteria and phages.

bacteria microbiome phage phage-bacteria-networks reproducible-paper

Last synced: 23 Feb 2026

https://github.com/uxxhans/rainbow-cats-microbiome-simulator

A small program that simulates organic patterns of microbiome.

microbiome organic-computing processing-library

Last synced: 10 Oct 2025

https://github.com/cafferychen777/microbiomestat-shiny

A Shiny interface for the MicrobiomeStat R package, designed to facilitate analysis and visualization of microbiome data.

longitudinal-data microbiome microbiome-analysis microbiome-data microbiome-workflow

Last synced: 07 Sep 2025

https://github.com/microbiome/miadash

Dashboard for microbiome data analysis with mia

bioinformatics dashboard gui isee mia microbiome shiny visualisation webapp

Last synced: 10 Apr 2025

https://github.com/earmingol/microbiome-factorization

Examples of using PhyloFactor and DEICODE to analyze microbiome datasets.

factorization factorization-methods machine-learning microbiome microbiome-datasets

Last synced: 24 Mar 2025

https://github.com/kronopt/simulate

Simulator of Antibiotic Therapy Effects on the Dynamics of Bacterial Populations

antibiotic-resistance bacteria enterotype kivy microbiome python python-2 simulation

Last synced: 03 Oct 2025

https://github.com/ebedthan/corebiota

Probabilistic partition of count data to identify core species

bioinformatics microbiome r

Last synced: 16 Mar 2025

https://github.com/cometsong/ma-genta

Targeted Probe Design Pipeline. Using mWGS genome bin clusters, prokka annotation predictions, and blast+ databases for generation, processing and filtering probe sequences.

annotation bioinformatics genome microbes microbiome ncbi-blast pipeline predictors probe sequence targeted

Last synced: 14 Mar 2025

https://github.com/saezlab/hepatic-microenviroment

Gut microbiota fuels HCC development by shaping the hepatic inflammatory microenvironment

cancer hcc liver microbiome r transcriptomics

Last synced: 22 Jul 2025

https://github.com/erictleung/microbetv-papers

:headphones: Papers discussed on various shows on MicrobeTV

bibtex immunology microbetv microbiome parasites podcast virology

Last synced: 18 Jan 2026

https://github.com/amnona/dbbact-calour

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

database microbiome microbiome-analysis

Last synced: 19 Jan 2026

https://github.com/thejacksonlaboratory/jaxid_generator

Microbiome-Core JAXid tracking ID code generator and view/search web app

django jackson-labs microbiome python3 tracking

Last synced: 20 May 2026

https://github.com/translator-catrax/multiomics_kg

Here are the configs for MultiomicsKG. Feel free to add or edit any of these as you see fit. There's a config checker and guidelines here too.

configuration knowledge-graph microbiome multiomics ncats-translator python3 tablassert yaml

Last synced: 21 May 2026

https://github.com/niaid/microbiome

Microbiome Data Analysis and Nephele Demo

bcbb-training microbiome microbiome-analysis

Last synced: 31 Jan 2026

https://github.com/dienerlab/pipelines

A monorepo containing all of our Nextflow pipelines.

metagenomics metatranscriptomics microbiome nextflow

Last synced: 02 Jun 2026

https://github.com/microbiome/miaDash

Dashboard for microbiome data analysis with mia

bioinformatics dashboard gui isee mia microbiome shiny visualisation webapp

Last synced: 27 Mar 2025

https://github.com/shandley/dada2-workflow

Generalized dada2 workflow. Refer to the wiki for help and troubleshooting.

16s 16s-rrna asv dada2 microbiome phyloseq

Last synced: 16 Feb 2026

https://github.com/biocore/q2-ili

QIIME2 plugin for `ili

microbiome qiime visualization

Last synced: 21 Apr 2026

https://github.com/waldronlab/bioanalyzer-backend

Streamline BugSigDB curation with AI-powered scientific paper analysis. Automatically extracts essential microbiome study metadata from research papers, reducing manual curation time and improving data quality for the BugSigDB database.

ai api bioinformatics microbiome ml ncbi paper-analysis python

Last synced: 08 Jun 2026

https://github.com/danedwardsdeveloper/plant-counter-iphone

iOS app for tracking your intake of plant food. Reached number 9 in the App Store food and drink category chart.

expo food health microbiome nativewind reactnative

Last synced: 14 May 2026

https://github.com/fredhutch/sti_crc_method_comparison

Chef Cookbook for configuring Microbiome Data Sharing Portal

chef-application chef-cookbook microbiome

Last synced: 25 Jun 2025