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Welcome to Epigenomics Workshop 2025!
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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.

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Thanks for visiting! Please note that as of 2026, the workshop homepage has moved to a new location, and this page will not be updated.

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Current Workshop Materials
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The workshop materials will be hosted on our `new homepage <https://nbisweden.github.io/workshop-epigenomics/>`_.





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Application
-----------


- Application is now open!
- Sign up `here <https://training.scilifelab.se/events/epigenomics-data-analysis-from-bulk-to-single-cell>`_.

.. - Application is now closed
.. - Sign up `here <https://forms.gle/BSieETwyWHACwRsT8>`_ and we will let you know when we open application for the next workshop.



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Date
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Please visit workshop current homepage for dates of upcoming events.

.. 22 - 26 September 2025



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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

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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 Programming Foundations for Life Scientists” or equivalent



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.. Application
.. -----------

.. - Application is now closed
.. - Sign up `here <https://forms.gle/ZE6DhAY22QhzFwVs5>`_. and we will let you know when we open application for the next course.


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Selection criteria
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 - 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 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.


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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.

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Computing Resources
--------------------------------

This workshop relies on HPC infrastructure kindly provided by `NAISS <https://www.naiss.se/>`_ via `Uppsala Multidisciplinary Center for Advanced Computational Science Uppmax <https://www.uppmax.uu.se/>`_.


Teaching team
-------------

- `Agata Smialowska <https://nbis.se/staff/agata-smialowska>`_ <agata.smialowska@nbis.se>

- Louella Vasquez <louella.vasquez@scilifelab.se>

- Dania Machlab <dania.machlab@scilifelab.se>

- Markus Ringnér <markus.ringner@scilifelab.se>

- `Simon Elsässer <https://www.scilifelab.se/researchers/simon-elsasser/>`_ <simon.elsasser@ki.se>

- Carmen Navarro Luzón <carmen.navarro@scilifelab.se>



.. - `Jessica Nordlund <https://katalog.uu.se/profile/?id=N8-1393>`_ <Jessica.Nordlund@medsci.uu.se>



.. - `Jakub Orzechowski Westholm <https://nbis.se/about/staff/jakub-orzechowski-westholm/>`_ <jakub.westholm@scilifelab.se>

.. - `Vincent van Hoef <https://nbis.se/about/staff/vincent-van-hoef>`_ <vincent.vanhoef@nbis.se>


.. - `Olga Dethlefsen <https://nbis.se/about/staff/olga-dethlefsen/>`_ <olga.dethlefsen@nbis.se>

.. - `Phil Ewels <https://www.kth.se/profile/phile?l=en>`_ <phil.ewels@scilifelab.se>



.. - `Harshil Patel <https://www.researchgate.net/profile/Harshil_Patel12>`_ <Harshil.Patel@crick.ac.uk>



Contact us
----------

- edu.epigenomics@nbis.se




Site Contents
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.. toctree::
   :maxdepth: 1

   content/precourse
   content/online-classroom
   content/schedule
   content/tutorials
   content/presentations