How to analyze a microbiome (edX)

How to analyze a microbiome (edX)
Course Auditing
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Basic knowledge of biology is required throughout the course. Basic knowledge of statistics and programming is required to complete specific sections of this course.
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How to analyze a microbiome (edX)
Learn common analysis techniques to make sense of microbial sequencing data. Microorganisms play a major role in the biosphere and within our bodies, but only a tiny fraction has been cultured so far. Microbiome data, that is the genetic information of microorganisms, is therefore an important window into the hidden microbial world.

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Microbiome data analysis elucidates the composition of microbial communities and how it changes in response to the environment. When analyzing sequencing data, we learn whether microbial diversity differs across conditions and identify links between microbes. In brief, microbiome data analysis gives us a first idea of how a microbial ecosystem works.



This course will illustrate with the help of real-world example data how to carry out typical analysis tasks, such as comparing microbial composition and diversity, clustering samples and computing associations. If you plan to work with microbiome data, this course will get you up to speed.

The instructors are experienced bioinformaticians who are internationally known for their analysis of large-scale microbiome data sets.


What you'll learn

- How and why microbiome data are collected

- How to extract species and function counts from sequencing data

- The definitions of richness, evenness and diversity

- How to compare diversity and microbial composition across conditions

- How to compute and interpret taxon and function associations


Syllabus


Module 0: Introduction

Study guide, R basics and a help forum for programming questions


Module 1: Introduction to microbiome data

Sequencing techniques, data types (16S, WGS, metadata), example applications


Module 2: From sequences to counts

Quality control of reads, taxonomic and functional assignment


Module 3: Comparing microbiomes

Relative versus absolute abundance, taxonomic and functional richness, evenness and diversity


Module 4: Ordination

Dimension reduction: arranging samples according to their taxonomic and functional composition in two-dimensional space


Module 5: Taxon/function associations

Network construction: computing and interpreting associations between taxa and functions


Module 6: Your favourite microbiome

Databases and journals for microbiome data and guidelines for doing your own analysis


Module 7: Final exam

Complete the course by passing the quiz or by completing a microbiome analysis



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Course Auditing
41.00 EUR
Basic knowledge of biology is required throughout the course. Basic knowledge of statistics and programming is required to complete specific sections of this course.

MOOC List is learner-supported. When you buy through links on our site, we may earn an affiliate commission.