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    42 repositories

    • miaViz

      Public
      Microbiome Analysis Plotting and Visualization
      visualizationbioconductorplottingmicrobiomemicrobiome-analysis
      R
      •
      Artistic License 2.0
      •11•10•11•2•Updated Oct 7, 2024Oct 7, 2024

    • mia

      Public
      Microbiome analysis
      analysisbioconductormicrobiome
      R
      •
      Artistic License 2.0
      •28•48•25•0•Updated Oct 7, 2024Oct 7, 2024

    • miaTime

      Public
      Microbiome time series analysis
      R
      •
      Artistic License 2.0
      •4•5•17•2•Updated Oct 7, 2024Oct 7, 2024

    • OMA

      Public
      Orchestrating Microbiome Analysis
      rbioconductormicrobiomemicrobiome-analysis-book
      TeX
      •43•86•34•3•Updated Oct 6, 2024Oct 6, 2024

    • iSEEtree

      Public
      extension of iSEE for TreeSE
      visualisationmicrobiomeshiny-apps
      R
      •2•3•2•1•Updated Oct 3, 2024Oct 3, 2024

    • 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" (September 2024), hosted by NCBI and NIAID.
      JavaScript
      •
      Artistic License 2.0
      •2•0•0•0•Updated Sep 27, 2024Sep 27, 2024

    • outreach

      Public
      Publications, slides, and posters
      HTML
      •3•0•2•0•Updated Sep 26, 2024Sep 26, 2024

    • microbiomeDataSets

      Public
      Experiment Hub based microbiome datasets
      bioconductormicrobiomemicrobiome-datasetsexperiment-hub
      R
      •4•5•0•0•Updated Sep 21, 2024Sep 21, 2024

    • miaSim

      Public
      microbiome data simulation package
      R
      •
      Artistic License 2.0
      •10•18•4•1•Updated Sep 21, 2024Sep 21, 2024

    • miaDemo

      Public
      Dockerfile
      •
      Other
      •2•1•0•0•Updated Sep 16, 2024Sep 16, 2024

    • microbiome.github.com

      Public
      microbiome project - home page
      HTML
      •3•1•1•0•Updated Aug 17, 2024Aug 17, 2024

    • data

      Public
      Microbiome datasets of the mia ecosystem
      R
      •2•0•0•1•Updated Apr 26, 2024Apr 26, 2024

    • qiime2R

      Public
      Import qiime2 artifacts to R
      HTML
      •
      MIT License
      •50•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
      •11•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

    • microbiome

      Public
      microbiome R package
      human-microbiomepopulation-studyhitchiphitchip-atlasrmicrobiologymicrobiomemicrobiome-analysisphyloseq
      R
      •
      Other
      •54•286•30•0•Updated Aug 4, 2023Aug 4, 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
      •28•1•0•0•Updated Jul 6, 2023Jul 6, 2023

    • course_2023_oulu

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

    • RPA

      Public
      Robust Probabilistic Averaging
      R
      •
      Other
      •0•1•0•0•Updated Apr 8, 2023Apr 8, 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 that data and analysis with others. See the phyloseq front page:
      R
      •187•2•0•0•Updated Mar 14, 2023Mar 14, 2023

    • scater

      Public
      Clone of the Bioconductor repository for the scater package.
      R
      •39•0•0•0•Updated Mar 9, 2023Mar 9, 2023

    • course_mia

      Public
      0•0•0•0•Updated Feb 19, 2023Feb 19, 2023

    • miacourse

      Public
      TeX
      •
      Other
      •0•1•0•0•Updated Feb 19, 2023Feb 19, 2023

    • dada2

      Public
      Accurate sample inference from amplicon data with single nucleotide resolution
      R
      •
      GNU Lesser General Public License v3.0
      •142•0•0•0•Updated Dec 10, 2022Dec 10, 2022

    • examples

      Public
      Example solutions to programming tasks
      0•0•0•0•Updated Nov 30, 2022Nov 30, 2022

    • course_2022_radboud

      Public
      Radboud summer school 2022
      TeX
      •
      Other
      •5•1•0•0•Updated Jul 11, 2022Jul 11, 2022

    • course_2022_oulu

      Public template
      TeX
      •
      Other
      •5•0•2•1•Updated Jul 10, 2022Jul 10, 2022

    • course_2022_turku

      Public
      TeX
      •
      Other
      •0•1•0•0•Updated May 17, 2022May 17, 2022

    • tutorials

      Public
      Tutorials
      HTML
      •
      Other
      •10•14•3•0•Updated Apr 2, 2022Apr 2, 2022