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01-program.Rmd
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# Program
The course takes place daily from 9am – 5pm (CEST), including
coffee and lunch breaks.
We expect that participants will prepare for the course in advance, see section
\@ref(start). Online support is available.
The material follows open online book created by the course teachers,
Orchestrating Microbiome Analysis
https://microbiome.github.io/OMA. This is R/Bioconductor framework for
multi-omic data science.
<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
**Morning session**
9-10 Coffee, Welcome & Practicalities
10-11 Lecture: Open & reproducible workflows
11-12 Demo & hands-on: Introduction to CSC RStudio notebook
12-13 Lunch break
**Afternoon hands-on session**
13-15 Demo: Data science framework
15-17 Hands-on: microbiome data summaries & exploration
17-18 Presentations & Discussion
----------------------------------------------------------------
## Day 2 - Tabular data
**Morning session**
9-10 Lecture: Analysis & visualization of _tabular data_
10-12 Demo & hands-on: Univariate methods
12-13 Lunch break
**Afternoon hands-on session**
13-14 Demo: Multivariate data analysis & visualization
14-17 Hands-on: Multivariate data analysis & visualization
17-18 Presentations & Discussion
----------------------------------------------------------------
## Day 3 - Multi-assay data
**Morning session**
9-10 Lecture: multi-omic data integration
10-12 Demo & hands-on: multi-assay data container
12-13 Lunch break
**Afternoon hands-on session**
13-15: Demo & hands-on: association analysis
13-17: Demo & hands-on: machine learning
17-18 Presentations & Discussion
-----------------------------------------------------------------
## Day 4 - Advanced topics
**Morning session**
9-10 Summary of the learning material
10-12 Demo & hands-on: custom data & advanced tools
12-13 Q & A session
**Afternoon session**
13-14 Lunch
14-16 Wrap-up