microbiome

All

44 repositories

mia
Public
Microbiome analysis
analysis bioconductor microbiome
R
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Artistic License 2.0
•27•52•25•2•Updated Feb 4, 2025Feb 4, 2025
miaTime
Public
Microbiome time series analysis
R
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Artistic License 2.0
•4•6•15•2•Updated Feb 4, 2025Feb 4, 2025
miaDash
Public
Dashboard for microbiome data analysis with mia
gui bioinformatics dashboard shiny visualisation webapp microbiome isee mia
R
•2•0•3•0•Updated Feb 4, 2025Feb 4, 2025
outreach
Public
Publications, slides, and posters
HTML
•3•0•2•0•Updated Feb 2, 2025Feb 2, 2025
RPA
Public
Robust Probabilistic Averaging
R
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Other
•0•1•0•0•Updated Jan 31, 2025Jan 31, 2025
miaViz
Public
Microbiome Analysis Plotting and Visualization
visualization bioconductor plotting microbiome microbiome-analysis
R
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Artistic License 2.0
•12•10•10•0•Updated Jan 30, 2025Jan 30, 2025
OMA
Public
Orchestrating Microbiome Analysis
r bioconductor microbiome microbiome-analysis-book
TeX
•44•89•33•4•Updated Jan 25, 2025Jan 25, 2025
miaDemo
Public
Dockerfile
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Other
•2•1•0•0•Updated Jan 9, 2025Jan 9, 2025
course_2024_oulu
Public
Oulu 2024 microbiome course
HTML
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Other
•1•0•0•0•Updated Jan 3, 2025Jan 3, 2025
iSEEtree
Public
extension of iSEE for TreeSE
visualisation microbiome shiny-apps
R
•2•3•3•0•Updated Dec 14, 2024Dec 14, 2024
microbiome
Public
microbiome R package
human-microbiome population-study hitchip hitchip-atlas r microbiology microbiome microbiome-analysis phyloseq
R
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Other
•55•290•30•0•Updated Dec 7, 2024Dec 7, 2024
data
Public
Microbiome datasets of the mia ecosystem
R
•3•0•0•1•Updated Nov 21, 2024Nov 21, 2024
miaSim
Public
microbiome data simulation package
R
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Artistic License 2.0
•10•20•4•0•Updated Oct 20, 2024Oct 20, 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
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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•5•0•0•Updated Sep 21, 2024Sep 21, 2024
microbiome.github.com
Public
microbiome project - home page
HTML
•3•1•1•0•Updated Aug 17, 2024Aug 17, 2024
qiime2R
Public
Import qiime2 artifacts to R
HTML
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MIT License
•53•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
•29•1•0•0•Updated Jul 6, 2023Jul 6, 2023
course_2023_oulu
Public
Oulu 2023 course
HTML
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Other
•1•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
•188•2•0•0•Updated Mar 14, 2023Mar 14, 2023
scater
Public
Clone of the Bioconductor repository for the scater package.
R
•40•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
•144•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
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Other
•5•1•0•0•Updated Jul 11, 2022Jul 11, 2022
course_2022_oulu
Public template
TeX
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Other
•5•0•2•1•Updated Jul 10, 2022Jul 10, 2022