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    50 repositories

    • daa

      Public
      R/Bioconductor package for differential abundance analysis (DAA).
      R
      •1•0•8•1•Updated Apr 16, 2026Apr 16, 2026

    • benchmarking

      Public
      Benchmarking miaverse performance
      R
      •
      Artistic License 2.0
      •0•1•2•0•Updated Apr 16, 2026Apr 16, 2026

    • mia

      Public
      Microbiome analysis
      analysisbioconductormicrobiome
      analysisbioconductormicrobiome
      R
      •
      Artistic License 2.0
      •34•55•36•9•Updated Apr 13, 2026Apr 13, 2026

    • OMA_manuscript

      Public
      BibTeX Style
      •12•0•6•2•Updated Apr 8, 2026Apr 8, 2026

    • OMA

      Public
      Orchestrating Microbiome Analysis
      rbioconductormicrobiome
      rbioconductormicrobiomemicrobiome-analysis-book
      TeX
      •55•108•39•7•Updated Mar 26, 2026Mar 26, 2026

    • OMA-extras

      Public
      Orchestrating Microbiome Analysis — extras
      TeX
      •55•0•0•1•Updated Mar 25, 2026Mar 25, 2026

    • miaViz

      Public
      Microbiome Analysis Plotting and Visualization
      visualizationbioconductorplotting
      visualizationbioconductorplottingmicrobiomemicrobiome-analysis
      R
      •
      Artistic License 2.0
      •14•12•13•6•Updated Mar 23, 2026Mar 23, 2026

    • multiomics

      Public
      R/Bioconductor package for multiomics integration
      R
      •0•0•0•0•Updated Mar 22, 2026Mar 22, 2026

    • outreach

      Public
      Publications, slides, and posters
      HTML
      •4•0•2•1•Updated Mar 15, 2026Mar 15, 2026

    • OMATutorials

      Public
      TeX
      •
      Other
      •2•2•0•0•Updated Dec 4, 2025Dec 4, 2025

    • data

      Public
      Microbiome datasets of the mia ecosystem
      R
      •6•0•3•2•Updated Nov 7, 2025Nov 7, 2025

    • HoloFoodR_manuscript

      Public
      TeX
      •0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • microbiome.github.com

      Public
      microbiome project - home page
      HTML
      •2•1•2•0•Updated Oct 18, 2025Oct 18, 2025

    • miaTime

      Public
      Microbiome time series analysis
      R
      •
      Artistic License 2.0
      •5•7•12•1•Updated Oct 14, 2025Oct 14, 2025

    • miaSim

      Public
      microbiome data simulation package
      R
      •
      Artistic License 2.0
      •8•22•4•0•Updated Oct 2, 2025Oct 2, 2025

    • workflows

      Public
      Microbiome workflows
      0•0•7•0•Updated Sep 29, 2025Sep 29, 2025

    • miaDash

      Public
      Dashboard for microbiome data analysis with mia
      guibioinformaticsdashboard
      guibioinformaticsdashboardshinyvisualisationwebappmicrobiomeiseemia
      R
      •4•1•7•0•Updated Sep 10, 2025Sep 10, 2025

    • iSEEtree

      Public
      extension of iSEE for TreeSE
      visualisationmicrobiomeshiny-apps
      visualisationmicrobiomeshiny-apps
      R
      •3•3•4•0•Updated Aug 29, 2025Aug 29, 2025

    • microbiome

      Public
      microbiome R package
      rmicrobiologymicrobiome
      rmicrobiologymicrobiomemicrobiome-analysisphyloseqhuman-microbiomepopulation-studyhitchiphitchip-atlas
      R
      •
      Other
      •57•314•30•0•Updated Aug 19, 2025Aug 19, 2025

    • RPA

      Public
      Robust Probabilistic Averaging
      R
      •
      Other
      •0•1•0•0•Updated Jan 31, 2025Jan 31, 2025

    • course_2024_oulu

      Public
      Oulu 2024 microbiome course
      HTML
      •
      Other
      •2•1•0•0•Updated Jan 3, 2025Jan 3, 2025

    • amr-2024-team-lahti

      Public
      This repository contains tools and resources developed by Team Lahti during the "Resistance is Futile: A Codeathon to Combat Antimicrobial Resistance" (Septembe…
      JavaScript
      •
      Artistic License 2.0
      •3•0•0•0•Updated Sep 27, 2024Sep 27, 2024

    • microbiomeDataSets

      Public
      Experiment Hub based microbiome datasets
      bioconductormicrobiomemicrobiome-datasets
      bioconductormicrobiomemicrobiome-datasetsexperiment-hub
      R
      •4•6•2•0•Updated Sep 21, 2024Sep 21, 2024

    • qiime2R

      Public
      Import qiime2 artifacts to R
      HTML
      •
      MIT License
      •52•0•0•0•Updated Apr 22, 2024Apr 22, 2024

    • MGnifyR

      Public
      R package for searching, downloading and analysis of EBI MGnify metagenomics data
      R
      •
      Artistic License 2.0
      •10•0•0•0•Updated Mar 28, 2024Mar 28, 2024

    • course_2023_bergen

      Public
      TeX
      •
      Other
      •0•0•0•0•Updated Oct 1, 2023Oct 1, 2023

    • bluster

      Public
      Clone of the Bioconductor repository for the bluster package.
      R
      •3•0•1•0•Updated Aug 2, 2023Aug 2, 2023

    • ANCOMBC

      Public
      Differential abundance (DA) and correlation analyses for microbial absolute abundance data
      R
      •33•1•0•0•Updated Jul 6, 2023Jul 6, 2023

    • course_2023_oulu

      Public
      Oulu 2023 course
      HTML
      •
      Other
      •2•0•0•0•Updated Jun 20, 2023Jun 20, 2023

    • phyloseq

      Public
      phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share…
      R
      •194•2•0•0•Updated Mar 14, 2023Mar 14, 2023
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