Epigenomics Data Analysis: from Bulk to Single Cell – ONLINE


Online event via Zoom

Epigenomics Data Analysis: from Bulk to Single Cell – ONLINE

September 16, 2024 @ 08:00 September 20, 2024 @ 17:00 CEST

National course open for PhD students, postdocs, researchers and other employees in all Swedish universities, in need of  Epigenomics data analysis skills. We also welcome applications from outside of Sweden and from the non-academic sector, for more info contact us!

Important dates and information

Application opens: 2024-04-26

Application closes: 2024-08-28

Confirmation to accepted students: 2024-08-30

Course Leaders : Agata Smialowska and Louella Vasquez

Contact information:  edu.epigenomics@nbis.se

Course fee

This online training event has no fee for academic participants. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2 000 SEK. For non-academic participants a course fee* of 12 000 SEK  will be invoiced.

*Please note that NBIS cannot invoice individuals

Course content

This workshop aims to introduce the best practice bioinformatics methods for processing, analyses, visualisation and integration of epigenomics and functional genomics data.

Topics covered include:

  • Data processing and analyses for differential DNA methylation with Illumina EPIC arrays and Bisulfite-seq;
  • ChIP-seq: peak calling, peak independent / dependent quality metrics, differential binding analysis; DNA motif enrichment;
  • ATAC-seq: peak calling, peak independent / dependent quality metrics, differential accessibility analysis;
  • Quantitative ChIP-seq using spike-ins;
  • CUT&Tag / CUT&RUN: Novel methods to investigate protein-chromatin interactions;
  • Functional analysis, including finding nearest genes and custom features, GO terms and Reactome pathways enrichment;
  • Basic multi-omics exploration and integration;
  • Visualisations of epigenomics datasets;
  • Introduction to analysis of single cell functional genomics data (scATAC-seq);
  • Introduction to nf-core pipelines for processing and analysis of epi- and functional genomics data : Methylseq, ChIP-seq, ATAC-seq.

Entry requirements

Required for being able to follow the workshop and complete the computer exercises:

  • BYOL, bring your own laptop with R and RStudio installed;
  • Basic knowledge in Linux;
  • Basic programming experience, preferably in R.


  • Experience working on the SNIC center Uppmax or another HPC. We encourage participants to run the linked Uppmax tutorial before the workshop;
  • Previous experience with NGS data analyses;
  • Completing NBIS workshops “Introduction to Bioinformatics using NGS data” and “R Foundations for Life Scientists” or equivalent.

Due to limited space the course can accommodate a maximum of 25 participants. If we receive more applications, participants will be selected based on selection criteria, including (but not limited to) correct entry requirements, motivation to attend the course, as well as gender and geographical balance.


Last updated: 2024-04-26

Content Responsible: Hampus Persson(hampus.persson@scilifelab.uu.se)