Introduction

Orchestrating Microbiome Analysis with Bioconductor

Introduces microbiome analysis framework
For participants with sufficient programming skills

Code of Conduct

Bioconductor community values an open approach to science that promotes

sharing of ideas, code, software and expertise
collaboration
diversity and inclusivity
a kind and welcoming environment
community contributions

By participating in this community, you agree not to engage in behavior contrary to these values at any Bioconductor-sponsored event or electronic communication channel.

For the full CoC, see: https://bioconductor.github.io/bioc_coc_multilingual

Schedule

Day 1 — Mon: Introduction to Bioconductor framework

Day 2 — Tue: Data wrangling

Day 3 — Wed: Community diversity & composition

Day 4 — Thu: Statistical testing

Day 5 — Fri: Advanced topics

Practicalities

Each topic: short lecture + demonstration
Majority of time: hands-on practice
Materials follow the “Orchestrating Microbiome Analysis” OMA online book
Slack channel: for real-time support
The openly licensed teaching material will be available online during and after the course

Questions

What are mia and OMA?
How microbiome data science is conducted in SummarizedExperiment ecosystem?
What benefits this new ecosystem have compared to previous approaches?

Learning goals

After the course, you will know how to:

Analyze microbiome data using the Bioconductor’s SummarizedExperiment ecosystem
Implement reproducible workflows
Explore documentation & tools via the OMA book

Learning goals for today

Broader context and practical skills on:

Bioconductor ecosystem
Data containers: understanding SummarizedExperiment
Importing data: how to get your data imported in R

Questions?

Moreno-Indias et al. (2021) Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology.