Version 20 (modified by rick, 7 years ago) (diff)


BBMRI omics Hands-on Course

date: March 31, 2017
Location: SURFsara, Utrecht
BBMRI url:


10:00-10:15 Introduction to available omics data within Description of RNA-seq, 450k methylation, metabolomics, imputed genotypes, phenotypes and technical covariates. Data location and access. (Rick Jansen)

10.15-10.45: Introduction to the BBMRIomics R package for integrated analysis of BBMRI-omics data using R (Maarten van Iterson)

10:45-11.45: Practicum (Maarten van Iterson)

11.45-12:30: Lunch (demo: using online atlases (Jan-Bert van Klinken))

12.30-13.00: Joost Verlouw: QTL lookup of GWAS hits. Take the SNP hits from a recent GWAS, extract corresponding BIOS genotype data, run association with full Methylation, Expression and Metabolomics data sets.

13.00-14.00: Practicum (Joost Verlouw)

14.00-14.15- Tea break

14:15-14:: Introduction to the Brainshake 1H-NMR metabolomics platform (Marian Beekman)

14:45-15.30: Practicum. Analyzing Metabolomics data (Koen Dekkers)

15:30-16:00: Allele specific expression (Niek de Klein & Freerk van Dijk)

16:00-17:00: Practicum (Niek de Klein & Freerk van Dijk))

17:00 Drinks

Practicum guidelines and exercises

Allele specific expression practicum is attached below.

Virtual machines used during the course

SSH connection

Rstudio connection

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