This virtual course will focus on microbiome data science with R/Bioconductor, a popular open-source environment for scientific data analysis. We will cover recommended open data science methods and workflows in microbiome research. After the course you will know how to approach new tasks in the analysis of taxonomic profiling data by taking advantage of available documentation and R tools.

Schedule 

Monday-Thursday 28.11-1.12.2022 at 9:00-12:30 Finnish time (8:00-11:30 Central European Time)

Teachers

Associate Prof., Leo Lahti and scientific programmer, Chouaib Benchraka
Department of Computing, University of Turku, Finland
datascience.utu.fi

Organized with the Finnish IT Center for Science (CSC).

Target audience

The course is primarily designed for advanced MSc, PhD and postdoctoral researchers who wish to learn new skills in scientific programming and multi-omic data analysis with a particular focus on microbiome research. Earlier experience with R is expected.

Structure of each day

Each day will include an overview lecture, supervised practical exercises and a joint demonstration session.

Program

Mon, Nov 28

Microbiome data access and quality control:
– reproducible reporting
– microbiome data containers
– microbiome data import
– microbiome data manipulation (subsetting, transformations, aggregation)
– microbiome data science workflow

Tue, Nov 29

Key concepts in microbiome data science:
– community diversity (alpha diversity)
– community similarity (beta diversity)
– visualization and exploration of tabular data

Wed, Nov 30

Community comparisons:
– differential abundance of individual taxa
– community-level comparisons 
– phylogeny-aware methods and balances

Thu, Dec 1

Advanced topics:
– time series analysis and visualization
– multi-omic data containers and exploration methods

Teaching material

The teaching follows the open online documentation created by the course teacher, extending the online book Orchestrating Microbiome Analysis (https://microbiome.github.io/OMA). The openly licensed teaching material, exercises and slides will be available online during and after the course.

Software

You will get temporary access to a cloud computing environment provided by CSC with preinstalled software packages. Instructions to access the environment will be sent to the registered participants. You are also encouraged to test the installation on your own system; limited support for this will be available.

Price

Course price is 120 (excluding VAT 24%) euros.

Important dates

• Application deadline: 28.10.2022
• Selection results will be announced by: 04.11.2022
• Selected participants need to register and pay by: 21.11.2022

Participants are selected based on the motivation description (use the fields, “Motivational description” and “Name of the group leader”) in the registration form.