Training
New measurement technologies and analysis methods keep coming and consequently the need for data analysis training is acute. Our efforts to plug the skills gap in single-cell and spatial omics analysis include:
As described in our white paper1, we aim at
“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 TeSS to establish a well-curated SCO training portal, listing national and international training providers, web resources and upcoming training events.”
Course Spatial transcriptomics data analysis
Workshop for Single-Cell Omics data analysis trainers
Workshop for Single-Cell RNA-seq data analysis trainers
Below you can find a list of course instances collected by the recent training survey conducted by the ELIXIR Single-Cell Omics Community. These courses have materials inc. slides and exercises available online, some of them provide recorded lectures too.
| Course name | Url | Course year | Duration | Single cell omics technologies | Spatial omics technologies |
|---|---|---|---|---|---|
| Single-cell RNA-seq data analysis using Chipster | Link | 2024 | 2 days | scRNAseq | |
| Visium data analysis with Chipster | Link | 2022 | 1 day | Spot based SRT e.g. 10X Visium | |
| MOOC Single-cell RNA-seq data analysis with Chipster | Link | 2024 | 3 days | scRNAseq | |
| Single-cell RNA-seq with R | Link | 2023 | 1 day | scRNAseq | |
| SincellTE: Single-Cell : Transcriptomics, Spatial and Multi-Omics | Link | 2022 | 5 days | scRNAseq, scATACseq, Multi modal Omics | Spot based SRT e.g. 10X Visium |
| Single Cell Galaxy Training | Link | 2021, 2023 | scRNAseq, scATACseq | ||
| Whole transcriptome data analysis | Link | 2023 | 5 days | scRNAseq | Spot based SRT e.g. 10X Visium |
| Análisis de datos transcriptómicos de célula única (scRNA-seq) con R y Bioconductor | Link | 2021 | 5 days | scRNAseq | Spot based SRT e.g. 10X Visium |
| Human Cell Atlas Latin America Single Cell RNA-seq Data Analysis Workshop | Link | 2021 | 5 days | scRNAseq | |
| Single cell RNA-seq data analysis with R | Link | 2019 | 2 days | scRNAseq | |
| Introduction to scRNAseq data analysis | Link | 5 days | scRNAseq | ||
| MGC/BioSB Course - Single Cell Analysis | Link | 2022 | 5 days | scRNAseq, Multi modal Omics | Spot based SRT e.g. 10X Visium |
| Analysis of single cell RNA-seq data | Link | Always online, last updated 2022 | scRNAseq | ||
| Workshop: Single-Cell RNA-Seq Analysis W20: Single-Cell RNA-Seq Analysis with R (note that there is also W20 with Python) | Link | 2021 | 1 day | scRNAseq | |
| Big-data and single-cell analysis for cancer research | Link | 2023 | 1 day | scRNAseq, CyTOF FACS, Multi modal Omics | |
| Single cell RNA-seq analysis workshop | Link | 2023 | 5 days | scRNAseq, CITEseq | |
| Spatial Omics Data Analysis | Link | 2023 | 5 days | scRNAseq | Spot based SRT e.g. 10X Visium, Image based SRT e.g. 10X Xenium ISS, Targeted proteomics SRT e.g. CODEX, Image analysis SRT e.g HE staining |
| Epigenomics Workshop | Link | 2023 | 5 days | scATACseq, scCHIPseq, scMETseq | |
| Advanced topics in Single Cell Omics | Link | 2021 | 5 days | scRNAseq, Multi modal Omics | Spot based SRT e.g. 10X Visium |
| Joint SIB and NBIS/SciLifeLab Autumn School Single Cell Analysis Course | Link | 2019 | 5 days | scRNAseq, CITEseq, CyTOF FACS, Multi modal Omics | Spot based SRT e.g. 10X Visium |
| Advanced topics in single-cell analysis | Link | 2022 | 4 days | scRNAseq, Multi modal Omics | Spot based SRT e.g. 10X Visium |
| Single Cell Transcriptomics | Link | 2023 | 3 days | scRNAseq, CITEseq, Multi modal Omics | |
| Introduction to single-cell RNA-seq data analysis | Link | 2023 | 3 days | scRNAseq | |
| 10X Single Cell RNA-Seq Analysis | Link | 2023 | 1 day | scRNAseq | |
| Advanced Single-Cell RNAseq Data Analysis 2023 | Link | 2023 | 3 days | scRNAseq, CyTOF FACS | |
| Introduction to Single-Cell RNAseq | Link | 2023 | 4 days | scRNAseq | |
| Single Cell Genomics - Latin America and the Caribbean | Link | 2023 | 5 days | scRNAseq | |
| Single Cell Technologies and Analysis | Link | 2022 | 5 days | scRNAseq, CyTOF FACS | |
| Single-Cell RNAseq Data Analysis 2022 | Link | 2022 | 4 days | scRNAseq | |
| Single-cell RNA-seq analysis using R | Link | 2022 | 5 days | scRNAseq | |
| Single-cell RNA-seq analysis using Galaxy | Link | 2023 | 5 days | scRNAseq | |
| Single cell RNA-seq analysis using Python | Link | 2023 | 5 days | scRNAseq | |
| 10X Single Cell RNA-Seq Analysis | Link | 2019 | 2 days | scRNAseq | |
| Single-cell RNA-seq data analysis workshop | Link | 2023 | 3 days | scRNAseq | |
| Single Cell ATAC-Seq Data Analysis | Link | 2023 | 2 days | scRNAseq | |
| Introduction to Single-cell RNA-Seq Workshop | Link | 2023 | 3 days | scRNAseq, CITEseq | |
| Advanced Single-cell Workshop | Link | 2023 | 5 days | scRNAseq, CITEseq |
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 ↩
