University of Oulu · Sep 28–30, 2026
From microbes
to multi-omics
Why are we here?
![Data and methods cycle]()
What you will learn
🔁
Reproducible
Transparent workflows with R and Quarto
📦
Standardized
Shared data containers for single- and multi-omics
🧭
Independent
Navigate documentation & existing tools for new tasks
You don’t need to know everything —
learn the ecosystem and how to navigate it.
Three days at a glance
Day 1
Open data science
Reproducible workflows with R/Bioconductor and Quarto
Day 2
Single omics
Tabular data analysis & visualization
Day 3
Multi-omics
Multi-assay data integration
Each topic: short lecture + demo, then mostly hands-on exercises — help is always available and materials stay online after the course.
Who’s who
Instructors
Leo Lahti
Tuomas Borman
Coordinator
Anna Kaisanlahti
Organizers
HBS-DP, University of Oulu Graduate School
Computing
CSC cloud services
For: MSc students, PhD candidates, postdocs and researchers building skills in R programming omics analysis visualization reproducible reporting
Open data science
Reproducible workflows with R/Bioconductor and Quarto
Day 1 — Schedule
| 9:00–10:00 |
☕ Coffee, welcome & practicalities |
| 10:00–11:00 |
Introduction to CSC RStudio notebook |
| 11:00–12:00 |
Lecture: open & reproducible workflows |
| 12:00–13:00 |
🍽️ Lunch break |
| 13:00–16:00 |
Working with data containers and workflows |
| Evening |
Informal course dinner (own cost) |
Day 1 — Goals
- Principles of open & reproducible microbiome / omics analysis
- The Bioconductor ecosystem
- Why standardized data containers matter
Microbiome research
- Microbiome: the community of microbes and their genes in a habitat (e.g. human gut)
- Vital role in health & environment
- Data: sequencing profiles + additional molecular layers
One container to hold it all
![TreeSummarizedExperiment structure]()
TreeSummarizedExperiment — assays, sample & feature data, trees in one object
Day 1 — Take-home
Reproducible reporting
Analyses become verifiable and easier to reuse, review and extend
TreeSE
TreeSummarizedExperiment is the standard container for microbiome data
Bioconductor
Interoperable packages built on shared data infrastructure
Single omics
Tabular data analysis & visualization
Day 2 — Schedule
| 9:00–10:00 |
Lecture: analysis & visualization of tabular data (single omics) |
| 10:00–12:00 |
Subsetting, transformations, and data summaries |
| 12:00–13:00 |
🍽️ Lunch break |
| 13:00–14:00 |
Univariate data analysis and visualization |
| 14:00–16:00 |
Multivariate data analysis and visualization |
Multi-omics
Multi-assay data integration
Day 3 — Schedule
| 9:00–10:00 |
Lecture: analysis & visualization of multi-assay data (multi-omics) |
| 10:00–12:00 |
Multi-assay data analysis and visualization |
| 12:00–13:00 |
🍽️ Lunch break |
| 13:00–15:00 |
Q&A and advanced techniques (time series, machine learning, simulation) |
| 15:00–16:00 |
Summary and wrap-up |
Linking the layers
MultiAssayExperiment links several omics layers measured on the same subjects.
microbiome metabolome transcriptome clinical
