Training
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.
Below you can find a list of course and other training-related events from our community.
ELIXIR-GOBLET Train-the-Trainer May 2023
Workshop for Single-Cell Omics data analysis trainers
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 |
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 https://doi.org/10.12688/f1000research.122312.1 ↩ ↩2 ↩3
