Bits & Bites #01: Short Course Series (Online)

Event Date


Bits & Bites # 01:

Network inference, visualization, and module detection in metabolomics data with Dr. Jan Krumsiek, Cornell University

Date: February 04, 2021

Instructor: Dr. Jan Krumsiek, Cornell University

Register here

Required software:

R, version 3.6.3 or higher

GeneNet package

igraph package

RCy3 package

Modentify package + dependencies:

Participant prerequisites: Basic knowledge of data analysis in R is required for this course, since we will directly start by reading a metabolomics data matrix and applying statistical models to it.Short description of the course: In this short course, we will implement typical steps of network analysis in metabolomics data. We will start from a metabolomics data matrix and walk through every step of the process, all the way to network visualizations and the identification of regulated network modules. For this, we will use Gaussian Graphical Models, a correlation-based statistical model which has been widely used in metabolomics datasets. The networks will be visualized using the igraph package and the RCy3 Cytoscape interface. A simple version of a module identification algorithm will be implemented from scratch. At the end of the course, the participants will be able to reproduce the major steps of network analysis contained in several publications from the Krumsiek lab.


More information: UC Davis offers 1-week and 2-week intensive courses in Metabolomics, but many researchers cannot contribute so much time! We therefore offer 'Bits and Bites' of some of our most popular parts of our intensive courses, see below. We hope to see you there! 

This 6-part short course series will feature in-depth topics in untargeted metabolomics such as pathway-based interpretation, Bayesian statistics, and a deeper look into MS-DIAL version 4.0. Each short course can be taken individually or you can select multiple Bites. Participants will gain a deeper insight into current software, methods, and pitfalls. Each session starts promptly at 9 a.m. (Pacific Time) and will take approx. 4 hours. The courses will be conducted in highly interactive manner, with use of freely available software and databases.  The tuition is $150 per Bite. We do offer a discounted price when you take 5 Bites for $700 or 6 Bites for $800.