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    91 repositories

    • kl-metapool

      Public
      Jupyter notebooks to assist with sample processing
      Python
      •
      MIT License
      •20•9•57•3•Updated Jan 16, 2026Jan 16, 2026

    • q2-katharoseq

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•1•1•3•Updated Jan 16, 2026Jan 16, 2026

    • emperor

      Public
      Emperor a tool for the analysis and visualization of large microbial ecology datasets
      visualizationpythonbioinformaticsmicrobiomeordinationemperorbiplots
      JavaScript
      •
      Other
      •49•54•63•1•Updated Jan 12, 2026Jan 12, 2026

    • microsetta-interface

      Public
      The Microsetta participant facing user interface
      Jinja
      •
      BSD 3-Clause "New" or "Revised" License
      •17•1•44•5•Updated Jan 6, 2026Jan 6, 2026

    • microsetta-private-api

      Public
      A private microservice to support The Microsetta Initiative
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •19•6•63•1•Updated Jan 6, 2026Jan 6, 2026

    • biom-format

      Public
      The Biological Observation Matrix (BIOM) Format Project
      Python
      •
      Other
      •93•96•25•3•Updated Dec 23, 2025Dec 23, 2025

    • pysyndna

      Public
      Python implementation and extension of SynDNA ("a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing", Zaramela et al., mSystems 2022
      Python
      •0•0•0•0•Updated Dec 12, 2025Dec 12, 2025

    • unifrac-binaries

      Public
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •9•2•4•0•Updated Dec 5, 2025Dec 5, 2025

    • gemelli

      Public
      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.
      ctfmicrobiomerpcaqiime2compositional-data-analysisrclrjoint-rpcatempted
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •19•85•35•3•Updated Nov 3, 2025Nov 3, 2025

    • micov

      Public
      Aggregate genome coverage
      Python
      •
      Other
      •6•10•12•1•Updated Oct 12, 2025Oct 12, 2025

    • unifrac

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •17•41•10•0•Updated Oct 10, 2025Oct 10, 2025

    • q2-conduit

      Public
      Plugin that converts Conduit metaproteomics results into QIIME 2 artifacts usable in downstream analyses
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Oct 8, 2025Oct 8, 2025

    • wol

      Public
      Reference Phylogeny for Bacterial and Archaeal Genomes
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •18•25•0•0•Updated Aug 9, 2025Aug 9, 2025

    • microsetta-processing

      Public
      Processing scripts for The Microsetta Initiative
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•1•1•Updated Jul 11, 2025Jul 11, 2025

    • microsetta-admin

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•0•16•3•Updated May 14, 2025May 14, 2025

    • improved-octo-waddle

      Public
      Balanced parentheses succinct data structure in Python
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •8•9•18•1•Updated Apr 18, 2025Apr 18, 2025

    • qurro

      Public
      Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples
      visualizationbioinformaticsmicrobiomeqiime
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •10•34•124•0•Updated Apr 4, 2025Apr 4, 2025

    • deblur

      Public
      Deblur is a greedy deconvolution algorithm based on known read error profiles.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •40•96•14•12•Updated Mar 8, 2025Mar 8, 2025

    • calour

      Public
      exploratory and interactive microbiome analyses based on heatmaps
      bioinformaticsheatmapjupyter-notebookmicrobiomeexploratory
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •21•27•62•5•Updated Jan 27, 2025Jan 27, 2025

    • q2-surpi

      Public
      A QIIME 2 plugin that connects SURPI+ results to QIIME 2 for analysis
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • q2-greengenes2

      Public
      A QIIME 2 plugin for interaction with the Greengenes2 database
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•33•7•0•Updated Oct 1, 2024Oct 1, 2024

    • Cq-VIEW

      Public
      A qPCR-based companion to the C-VIEW (COVID-19 VIral Epidemiology Workflow) pipeline that calculates samples' viral loads.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 26, 2024Sep 26, 2024

    • empress

      Public
      A fast and scalable phylogenetic tree viewer for microbiome data analysis
      visualizationbioinformaticsmicrobiomeordinationphylogenyqiimebiplotqiime2tree-plot
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •32•55•143•8•Updated Aug 4, 2024Aug 4, 2024

    • qadabra

      Public
      Snakemake workflow for comparison of differential abundance ranks
      workflowmachine-learningbioinformaticssnakemakepipelinemetagenomicsmicrobiomedifferential-abundance
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•13•11•0•Updated Mar 22, 2024Mar 22, 2024

    • tcga

      Public
      Microbial analysis in TCGA data
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •46•94•2•6•Updated Feb 23, 2024Feb 23, 2024

    • BIRDMAn

      Public
      Bayesian Inferential Regression for Differential Microbiome Analysis
      pythonbioinformaticsregressionbayesian-inferencestanmicrobiome
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•23•20•1•Updated Dec 19, 2023Dec 19, 2023

    • pynast

      Public archive
      Python Nearest Alignment Space Termination tool (PyNAST): Official repository for software and unit tests
      Python
      •
      Other
      •3•9•8•0•Updated Oct 30, 2023Oct 30, 2023

    • redbiom

      Public
      Sample search by metadata and features
      bioinformaticsmicrobiomeqiimebiom
      Python
      •
      Other
      •18•47•25•0•Updated Aug 31, 2023Aug 31, 2023

    • mustached-octo-ironman

      Public
      Easy dispatched compute in a Tornado environment
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•7•2•Updated Aug 14, 2023Aug 14, 2023

    • absquant

      Public
      Python
      •0•0•0•0•Updated Aug 14, 2023Aug 14, 2023