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

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

Virtual Event Virtual Event

October 25 @ 08:00 October 29 @ 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: 2021-10-10
Confirmation to accepted students:  2021-10-14

Responsible teachers

Agata Smialowska, Olga Dethlefsen, Jakub Westholm
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 and integration of epigenomics and functional genomics data.

Topics covered include

Data processing and analyses for differential methylation with Illumina EPIC arrays and Bisulfite-seq;
ChIP-seq and ATAC-seq: peak calling, peak independent/dependent quality metrics, differential binding and differential accessibility analysis; motif enrichment;
Functional analysis, including finding nearest genes and custom features, over-represented GO terms and Reactome pathways;
Advanced ChIP methods: CUT&RUN, CUT&Tag, use of spike-ins in ChIP-seq;
Integrative visualisations of epigenomics datasets;
Introduction to nf-core pipelines for processing and analysis of epi- and functional genomics data.
Basic multi-omics exploration and integration;
Introduction to analysis of single cell functional genomics data (scATAC-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.

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 course application, whether the course is valid for formal credits or not.

Last updated: 2021-10-27

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