Epigenomics Data Analysis: from Bulk to Single Cell (ONLINE)

September 18, 2023 September 22, 2023


Online event via Zoom

Epigenomics Data Analysis: from Bulk to Single Cell (ONLINE)

September 18 @ 08:00 September 22 @ 17:00 CEST

National workshop open for PhD students, postdocs, researchers and other employees within Swedish academia. This course is run by the National Bioinformatics Infrastructure Sweden (NBIS).

Important dates

Application opens:  now

Application closes: 2023-09-04

Confirmation to accepted students: 2023-09-08

Responsible teachers

Agata Smialowska, Jakub Orzechowski Westholm, Vincent van Hoef

Please contact edu.epigenomics@nbis.se for course specific questions

Workshop fee

This online training event has no fee. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK. 

*Please note that NBIS cannot invoice individuals.

Workshop 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 Programming Foundations for Life Scientists” or equivalent.

Due to limited capacity the workshop 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 workshop as well as gender and geographical balance.

Please note that NBIS training events do not provide any formal university credits.

This training content is estimated to correspond to a 1.5 HPs, however the estimated credits are just guidelines. If formal credits are crucial, participants need to confer with the home department whether the course is valid for formal credits.

Last updated: 2023-05-10

Content Responsible: Maria Bäckström(maria.backstrom@scilifelab.uu.se)