01-program.Rmd

# Program {#program}

The course takes place daily from 9am – 5pm (CEST), including coffee,
lunch, and short breaks. Most of the time will be dedicated to
practical exercises, complemented by short lectures and demos.

We expect that participants will prepare for the course in advance.
Instructions will be sent to the registered participants. Online
support is available.

The material follows open online book created by the course teachers,
[Orchestrating Microbiome Analysis](https://microbiome.github.io/OMA),
which supports R/Bioconductor framework for multi-omic data
integration and analysis.

<img src="fig.png" alt="ML4microbiome" width="50%"/>
<p style="font-size:12px">Figure source: Moreno-Indias _et al_. (2021) [Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions](https://doi.org/10.3389/fmicb.2021.635781). Frontiers in Microbiology 12:11.</p>


## Day 1 - Open data science 

Reproducible workflows with R/Bioconductor and Quarto 

**Morning**

10-11 Coffee, Welcome & Practicalities

11-12 Learning environment (CSC RStudio notebook and reproducible reporting with Quarto)

12-13 Lunch break

**Afternoon**

13-14 Lecture: open data science

14-16 Working with data containers and workflows 

16-17 Q & A

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## Day 2 - Tabular data analysis

**Morning**

 9-10 Lecture: analysis & visualization of _tabular data_ (single omics)

10-12 Data wrangling, exploration, and summaries

12-13 Lunch break

**Afternoon**

13-14 Univariate data analysis and visualization

14-16 Multivariate data analysis and visualization

16-17 Q & A

**Evening**

Course dinner (optional; own cost)

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## Day 3 - Multi-assay data integration 

**Morning**

 9-10 Lecture: analysis & visualization of _multi-assay data_ (multi-omics)

10-12 Multi-assay data analysis and visualization

12-13 Lunch break


**Afternoon**

13-15: Advanced methods (e.g. time series, machine learning, simulation)

15-16: Summary and wrap-up

16-17: Q & A