microbiome

All

45 repositories

miaTime
Public
Microbiome time series analysis
R
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Artistic License 2.0
•6•7•13•3•Updated Aug 22, 2025Aug 22, 2025
outreach
Public
Publications, slides, and posters
HTML
•3•0•2•0•Updated Aug 19, 2025Aug 19, 2025
microbiome
Public
microbiome R package
human-microbiome population-study hitchip hitchip-atlas r microbiology microbiome microbiome-analysis phyloseq
R
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Other
•56•304•30•0•Updated Aug 19, 2025Aug 19, 2025
OMA
Public
Orchestrating Microbiome Analysis
r bioconductor microbiome microbiome-analysis-book
TeX
•52•101•26•6•Updated Aug 17, 2025Aug 17, 2025
mia
Public
Microbiome analysis
analysis bioconductor microbiome
R
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Artistic License 2.0
•32•53•23•5•Updated Aug 17, 2025Aug 17, 2025
OMA_manuscript
Public
BibTeX Style
•8•0•12•4•Updated Aug 16, 2025Aug 16, 2025
benchmarking
Public
Benchmarking miaverse performance
R
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Artistic License 2.0
•0•1•1•0•Updated Aug 12, 2025Aug 12, 2025
miaViz
Public
Microbiome Analysis Plotting and Visualization
visualization bioconductor plotting microbiome microbiome-analysis
R
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Artistic License 2.0
•13•11•11•5•Updated Jul 30, 2025Jul 30, 2025
miaSim
Public
microbiome data simulation package
R
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Artistic License 2.0
•9•22•4•0•Updated Jul 28, 2025Jul 28, 2025
miaDash
Public
Dashboard for microbiome data analysis with mia
gui bioinformatics dashboard shiny visualisation webapp microbiome isee mia
R
•4•1•7•0•Updated Jul 25, 2025Jul 25, 2025
OMATutorials
Public
TeX
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Other
•2•2•0•0•Updated Jun 22, 2025Jun 22, 2025
data
Public
Microbiome datasets of the mia ecosystem
R
•4•0•0•0•Updated May 27, 2025May 27, 2025
iSEEtree
Public
extension of iSEE for TreeSE
visualisation microbiome shiny-apps
R
•3•3•3•0•Updated May 9, 2025May 9, 2025
RPA
Public
Robust Probabilistic Averaging
R
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Other
•0•1•0•0•Updated Jan 31, 2025Jan 31, 2025
course_2024_oulu
Public
Oulu 2024 microbiome course
HTML
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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" (September 2024), hosted by NCBI and NIAID.
JavaScript
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Artistic License 2.0
•3•0•0•0•Updated Sep 27, 2024Sep 27, 2024
microbiomeDataSets
Public
Experiment Hub based microbiome datasets
bioconductor microbiome microbiome-datasets experiment-hub
R
•4•6•1•0•Updated Sep 21, 2024Sep 21, 2024
microbiome.github.com
Public
microbiome project - home page
HTML
•3•1•2•1•Updated Aug 17, 2024Aug 17, 2024
qiime2R
Public
Import qiime2 artifacts to R
HTML
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MIT License
•54•0•0•0•Updated Apr 22, 2024Apr 22, 2024
MGnifyR
Public
R package for searching, downloading and analysis of EBI MGnify metagenomics data
R
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Artistic License 2.0
•10•0•0•0•Updated Mar 28, 2024Mar 28, 2024
course_2023_bergen
Public
TeX
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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
•30•1•0•0•Updated Jul 6, 2023Jul 6, 2023
course_2023_oulu
Public
Oulu 2023 course
HTML
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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 that data and analysis with others. See the phyloseq front page:
R
•190•2•0•0•Updated Mar 14, 2023Mar 14, 2023
scater
Public
Clone of the Bioconductor repository for the scater package.
R
•41•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
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Other
•0•1•0•0•Updated Feb 19, 2023Feb 19, 2023
dada2
Public
Accurate sample inference from amplicon data with single nucleotide resolution
R
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GNU Lesser General Public License v3.0
•154•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