Welcome to Epigenomics Workshop 2024!

Epigenomics Data Analysis: from Bulk to Single Cell

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

This workshop is an introduction to best practice bioinformatics methods for processing, analyses and integration of epigenomics data. The online teaching includes lectures, programming tutorials and interactive group sessions.



16th - 20nd September 2024



Application is now open here


Workshop content

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;

  • Integrative visualisations of epigenomics datasets;

  • Quantitative ChIP-seq;

  • 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;

  • Introduction to analysis of single cell functional genomics data (scATAC-seq);

  • Nf-core pipelines: Methylseq, ChIP-seq, ATAC-seq


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 Programming Foundations for Life Scientists” or equivalent


Selection criteria

  • Due to limited capacity the workshop can accommodate maximum of 30 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.

  • 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.


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 workshops and award 1.5 HPs, corresponding to 40 h of studying. It is up to participants to clarify and arrange credit transfer with the relevant university department.


Computing Resources

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

Teaching team

Contact us

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