OMA

Bioconductorproject

Orchestrating Microbiome Analysis with Bioconductor

R/Bioconductor packages and an online book for the statistical analysis of microbiome data, developed by the OMA consortium.

Read the book Get the packages

The book

Orchestrating Microbiome Analysis with Bioconductor covers the whole workflow, from data import and wrangling to diversity, differential abundance, multi-omics integration and machine learning, with reproducible examples on real data. It is free to read online.

Open the book

BiocManager::install(c("mia", "miaViz"))

library(mia)
library(miaViz)

data("GlobalPatterns", package = "mia")
tse <- GlobalPatterns

tse <- transformAssay(tse, method = "relabundance")
tse <- addAlpha(tse, index = "shannon")
plotAbundanceDensity(tse, n = 10)

Workshops

We teach microbiome data science with OMA at conferences, summer schools, universities and companies. Drag or zoom the globe to explore, or pick a workshop from the list.

Ctrl + scroll to zoom

24 workshops

● Registration open ● Upcoming ● Past

Microbiome data science workshopWorkshop · Feb 2027 · Malaysia
Microbiome data science workshopWorkshop · Nov 2026 · Addis Ababa, Ethiopia
TNO courseWorkshop · Oct 2026 · Leiden, Netherlands
Oulu doctoral school courseCourse · Sep 2026 · Oulu, Finland
ECCB2026Workshop · Sep 2026 · Geneva, Switzerland
BioC2026Workshop · Aug 2026 · Seattle, USA
Carpentries workshop (pre-EuroBioC2026)Carpentries workshop · Jun 2026 · Turku, Finland
Bioconductor webinarWebinar · May 2026 · Online
Physalia courseCourse · Feb 2026 · Online
Bioinformatics and a changing society seminarWorkshop · Dec 2025 · Turku, Finland
BioCAsia 2025Workshop · Nov 2025 · Adelaide, Australia
Metagenomic Bioinformatics in MGnifyCourse lecture · Oct 2025 · Hinxton, UK
EuroBioC2025Workshop · Sep 2025 · Barcelona, Spain
OMA summer schoolSummer school · Aug 2025 · Singapore, Singapore
Brain, bacteria, behavior summer courseSummer school · 2025 · Nijmegen, Netherlands
GBCC2025Training session · Jun 2025 · New York, USA
Bioconductor microbiome courseWorkshop · Apr 2025 · Belo Horizonte, Brazil
ECCB2024Workshop · Sep 2024 · Turku, Finland
Winter schoolWinter school · 2024 · Oulu, Finland
BioC2023Workshop · Aug 2023 · Boston, USA
Multi-omics courseCourse · Jun 2023 · Oulu, Finland
CSC training courseCourse · Nov 2022 · Espoo, Finland
Summer schoolSummer school · 2022 · Oulu, Finland
ML4MicrobiomeWorkshop · 2022 · Barcelona, Spain

Would you like a workshop for your group or event? Get in touch.

Publications

Preprint

Orchestrating Microbiome Analysis with Bioconductor
Borman T, Benedetti G, Muluh G, … OMA consortium, … Bastiaanssen TFS, Mallick H, Lahti L.
bioRxiv 2025 · doi:10.1101/2025.10.29.685036

Data container

TreeSummarizedExperiment: a S4 class for data with hierarchical structure
Huang R, Soneson C, Ernst FGM, Rue-Albrecht KC, Yu G, Hicks SC, Robinson MD.
F1000Research 9:1246, 2021 · doi:10.12688/f1000research.26669.2

If you use OMA in your work, please cite the preprint.

Contributors

OMA is developed by the OMA consortium. Questions and ideas are welcome in the #miaverse channel on Bioconductor Zulip, and contributions to the packages and the book through GitHub.

NANalin Arora TBThomaz Bastiaanssen MBMoritz E. Beber ABAituar Bektanov Giulio Benedetti SBSabuj Bhowmick Tuomas Borman DBDomenick J. Braccia HBHéctor Corrada Bravo MCMatteo Calgaro DCDanielle Callan JCJiya Chaudhary SDSneha Das BDBasil Courbayre Dussau HEHenrik Eckermann PEPande Erawijantari Felix G.M. Ernst EGElliot Gaudron-Parry SGShyam Gopalakrishnan MHMaija Hakula KHKati Hanhineva AHAki Havulinna RHRasmus Hindström AJAkewak Jeba Leo Lahti MLMorten Limborg HLHimmi Lindgren YLYihan Liu HMHimel Mallick CMCameron Martino DMDattatray Mongad CMChristian L. Müller GMGeraldson Muluh SNSigne Nynäs JPJesse Pasanen JPJuho Pelto SPStefanie Peschel RPRenuka Potbhare TPThéotime Pralas Marcel Ramos ARAura Raulo ASArtur Sannikov JSJoao Paulo Casucci dos Santos ESEly Seraidarian JSJacques Serizay LSLiat Shenhav SSSudarshan Shetty RSRajesh Shigdel VSVilhelm Suksi ETEetu Tammi BVBenjamin Valderrama BVBianca Cordazzo Vargas Levi Waldron LYLu Yang

Missing from the list? Add yourself to data/contributors.csv.