Workshop in Epigenomics Data Analysis


Epigenomics Data Analysis: from Bulk to Single Cell


16 - 20 September 2024 (ONLINE)
Course Info

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Application opens: 2024-04-26

Application closes: 2024-08-28

Confirmation to accepted students: 2024-08-30


The aim of this workshop is to introduce best practice bioinformatics methods for processing, analyses and integration of epigenomics data. The online teaching includes lectures, programming tutorials and interactive group sessions. This workshop is run by the National Bioinformatics Infrastructure Sweden (NBIS).

Audience Course open to PhD students, postdocs, and other researchers in all Swedish universities.  We also welcome applications from outside of Sweden and from the non-academic sector, for more info contact us!

Fee This online training event has no fee for academic participants. However, if you confirm your participation but do not do so (no-show) you will be invoiced 2000 SEK.   For non-academic participants, a course fee* of  12 000 SEK will be invoiced.   

*Please note that NBIS cannot invoice individuals.

By accepting to participate in the course, you will be agreeing to follow the NBIS Training Code of Conduct.


Covered topics

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

Topis 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;
  • Functional analysis, including finding nearest genes and custom features, GO terms and Reactome pathways enrichment;
  • Quantitative ChIP-seq;
  • CUT&Tag / CUT&RUN: Novel methods to investigate protein-chromatin interactions;
  • Integrative visualisations of epigenomics datasets;
  • Basic multi-omics exploration and integration;
  • Introduction to analysis of single cell functional genomics data (scATAC-seq);
  • Nf-cores pipelines: Methylseq, ChIP-seq, ATAC-seq



This is a national course. The course is open for PhD students, postdocs, group leaders and core facility staff. NBIS prioritises academic participants, especially PhD students, affiliated with Swedish universities. We warmly welcome international and/or non-academic participants when we have seats available and the requirements criteria are met.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

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Entry requirements

Required to be able to follow the tutorials:

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

Makes learning experience easier:

  • Experience working on the SNIC center Uppmax or another HPC
  • 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 maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.


Certificate & University credits

We will issue a course certificate upon a successful course completion, assessed by active participation in all course sessions (lectures, computer practicals, group discussion etc.).

Unfortunately we are not able to warrant any university credits (högskolepoäng). Many universities however, recognize the attendance in our courses and award 1.5 HPs, corresponding to a 40 h of studying. It is up to participants to clarify and arrange credit transfer with the relevant university department.



The course schedule can be found here.


Precourse material

Please read carefully the precourse materials prior to starting the course.


Teaching Team

Agata Smialowska, Louella Vasquez, Markus Ringnér, Simon Elsässer, Carmen Navarro Luzón

For any queries, please contact


   Computing Resources

This workshop relies on HPC infrastructure kindly provided by NAISS  via Uppsala Multidisciplinary Center for Advanced Computational Science Uppmax.

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CC attribution share alike This course content is offered under a CC attribution share alike license. Content in this course can be considered under this license unless otherwise noted.