Building capacity in Single-Cell and Spatial Omics

Our Goals

Our main goals regarding training are:

“Upskilling scientists in SCO data analysis and standards lies at the heart of the ELIXIR SCO Community, and particular efforts will be made to make the training scalable and FAIR in coordination with the ELIXIR Training platform. The SCO Community will ensure that training materials and expertise are shared efficiently and following FAIR and open research principles. We will collaborate with ELIXIR’s Training Portal TeSS65 to establish a well-curated SCO training portal, listing national and international training providers, web resources and upcoming training events.” 1

Please refer to our white paper1, where we describe and identify the challenges related to training in Single-Cell and Spatial Omics, and how our community will help fill those needs.

Our training events

Below you can find a list of course and other training-related events from our community.

ELIXIR-GOBLET Train-the-Trainer May 2023

  • Go to event page
  • Online
  • This course has been postponed to Q4/2023. More information will be displayed here in due time.

Workshop for Single-Cell Omics data analysis trainers

Existing materials

Below you can find a list of course instances provided by the collaboration between ELIXIR nodes 1:

Course                               Link ELIXIR node Training style Computing Language Recorded lectures FAIR Tool Length Technologies
Advanced topics in single cell omics (2021) link SE, CH PBL R and python Yes Docker 5 days scRNAseq, scATACseq, ST, Deep Learning
Single Cell School (2019) link SE, CH Tutorial R No 5 days - scRNAseq, CyTOF, scProteomics
Galaxy single-cell omics training materials (ongoing) link DE, UK, CH Tutorial - Yes Galaxy 3-5 days scRNAseq
Single-cell RNAseq analysis using R (2021) link UK EMBL-EBI Tutorial R No - 5 days scRNAseq
Gene Expression at Spatial Resolution (2021) link EMBL-EBI SE Tutorial - Yes - 4 Days Spatial transcriptomics (10X Visium)
Single-cell RNAseq data analysis with R (2019) link FI, SE, NL, DE, NO, FR Tutorial R Yes Conda 3 days scRNAseq
Single-cell RNAseq data analysis with Chipster (2020) link FI, LU Tutorial - Yes Chipster 3 days scRNAseq
Single-cell RNAseq data analysis with Chipster (ongoing) link FI, NL, SE, FR Tutorial, eLearning - Yes Chipster 3 days scRNAseq
Single cell RNA-seq analysis workshop (2022) link SE, NL Tutorial R and Python Yes Conda 5 days scRNAseq, ST


  1. Czarnewski P, Mahfouz A, Calogero RA et al. Community-driven ELIXIR activities in single-cell omics [version 1; peer review: awaiting peer review]. F1000Research 2022, 11(ELIXIR):869  2 3