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Expand Up @@ -54,23 +54,52 @@ Below you can find a list of course and other training-related events from our c

## Existing materials

Below you can find a list of course instances provided by the collaboration between ELIXIR nodes [^1]:
Below you can find a list of course instances collected by the recent SCO ELIXIR community survey:

<br>

<div class="SCO_training_table">

|Course&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; | Link | ELIXIR&nbsp;node | Training style | Computing Language | Recorded lectures | FAIR Tool | Length | Technologies|
| :- | :-: | :-: | :-: | :-: | :-: | :-: | :-: | :-: |
| **Advanced topics in single cell omics** (2021)| [link](https://nbisweden.github.io/single-cell_sib_scilifelab_2021/README.html) | SE, CH | PBL | R and python | Yes | Docker | 5 days | scRNAseq, scATACseq, ST, Deep Learning |
| **Single Cell School** (2019)| [link](https://nbisweden.github.io/single-cell_sib_scilifelab/) | SE, CH | Tutorial | R | No | 5 days | - | scRNAseq, CyTOF, scProteomics|
| **Galaxy single-cell omics training materials** (ongoing)| [link](https://training.galaxyproject.org/training-material/search?query=single-cell) | DE, UK, CH | Tutorial | - | Yes | Galaxy | 3-5 days | scRNAseq |
| **Single-cell RNAseq analysis using R** (2021) | [link](https://www.ebi.ac.uk/training/events/single-cell-rna-seq-analysis-using-r-virtual/) | UK EMBL-EBI | Tutorial | R | No | - | 5 days | scRNAseq |
| **Gene Expression at Spatial Resolution** (2021)| [link](https://www.embl.org/about/info/course-and-conference-office/events/spa21-01/) | EMBL-EBI SE | Tutorial | - | Yes | - | 4 Days | **Spatial transcriptomics** (10X Visium) |
| **Single-cell RNAseq data analysis with R** (2019)| [link](https://www.csc.fi/web/training/-/scrnaseq)| FI, SE, NL, DE, NO, FR |Tutorial| R |Yes |Conda |3 days |scRNAseq|
| **Single-cell RNAseq data analysis with Chipster** (2020)| [link](https://elixir-luxembourg.org/events/2020_10_27_scRNA_seq_with_Chipster) |FI, LU | Tutorial| - |Yes| Chipster |3 days |scRNAseq|
| **Single-cell RNAseq data analysis with Chipster** (ongoing)| [link](https://e-learn.csc.fi/course/view.php?id=17) |FI, NL, SE, FR |Tutorial, eLearning| - |Yes |Chipster |3 days|scRNAseq|
| **Single cell RNA-seq analysis workshop** (2022)| [link](https://uppsala.instructure.com/courses/52011) | SE, NL| Tutorial| R and Python| Yes| Conda |5 days |scRNAseq, ST|
|Course name |Url |Course year |Duration |Single cell omics technologies |Spatial omics technologies |
|:--------------------------------------------------------------------------------------------------------------------------|:-----|:--------------------------------|:--------|:-------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------|
|Single-cell RNA-seq data analysis using Chipster |[Link](https://chipster.rahtiapp.fi/manual/courses.html#single-cell)|2023 |2 days |scRNAseq | |
|Visium data analysis with Chipster |[Link](https://chipster.rahtiapp.fi/manual/courses.html#visium)|2022 |1 day | |Spot based SRT e g 10X Visium |
|MOOC Single-cell RNA-seq data analysis with Chipster |[Link](https://e-learn.csc.fi/course/view.php?id=17)|2023 |3 days |scRNAseq | |
|Single-cell RNA-seq with R |[Link](https://version.helsinki.fi/csc-courses/scrnaseq-with-r-2023/-/blob/main/README.md)|2023 |1 day |scRNAseq | |
|SincellTE: Single-Cell : Transcriptomics, Spatial and Multi-Omics |[Link](https://www.france-bioinformatique.fr/formation/single-cell-2022/)|2022 |5 days |scRNAseq, scATACseq, Multi modal Omics |Spot based SRT e g 10X Visium |
|Single Cell Galaxy Training |[Link](https://training.galaxyproject.org/training-material/topics/single-cell/)|2021, 2023 | |scRNAseq, scATACseq | |
|Whole transcriptome data analysis |[Link](https://www.embl.org/about/info/course-and-conference-office/events/dat23-01/)|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](https://comunidadbioinfo.github.io/cdsb2021_scRNAseq/)|2021 |5 days |scRNAseq |Spot based SRT e g 10X Visium |
|Human Cell Atlas Latin America Single Cell RNA-seq Data Analysis Workshop |[Link](https://www.humancellatlas.org/hca-latin-america-2021-workshop/)|2021 |5 days |scRNAseq | |
|Single cell RNA-seq data analysis with R |[Link](https://nbisweden.github.io/excelerate-scRNAseq/)|2019 |2 days |scRNAseq | |
|Introduction to scRNAseq data analysis |[Link](https://github.com/scgenomics/scgenomics-public.github.io (in house course))| |5 days |scRNAseq | |
|MGC/BioSB Course - Single Cell Analysis |[Link](https://github.com/LeidenCBC/MGC-BioSB-SingleCellAnalysis2022)|2022 |5 days |scRNAseq, Multi modal Omics |Spot based SRT e g 10X Visium |
|Analysis of single cell RNA-seq data |[Link](https://www.singlecellcourse.org/)|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](https://www.youtube.com/watch?v=jwSPTgF9ESQ&list=PLOXLw2he7kYpqAL0Gzco5NkA2DpewtluK)|2021 |1 day |scRNAseq | |
|Big-data and single-cell analysis for cancer research |[Link](https://stratagem-cost.eu/pandora-core-e-learning-platform-on-mdr-tumours/)|2023 |1 day |scRNAseq, CyTOF FACS, Multi modal Omics | |
|Single cell RNA-seq analysis workshop |[Link](https://github.com/NBISweden/workshop-scRNAseq)|2023 |5 days |scRNAseq, CITEseq | |
|Spatial Omics Data Analysis |[Link](https://github.com/NBISweden/workshop-spatial)|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](https://nbis-workshop-epigenomics.readthedocs.io/en/latest/content/schedule.html)|2023 |5 days |scATACseq, scCHIPseq, scMETseq | |
|Advanced topics in Single Cell Omics |[Link](https://nbisweden.github.io/single-cell_sib_scilifelab_2021/README.html)|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](https://nbisweden.github.io/single-cell_sib_scilifelab/)|2019 |5 days |scRNAseq, CITEseq, CyTOF FACS, Multi modal Omics |Spot based SRT e g 10X Visium |
|Advanced topics in single-cell analysis |[Link](https://www.sib.swiss/training/course/20220426_ADVSC)|2022 |4 days |scRNAseq, Multi modal Omics |Spot based SRT e g 10X Visium |
|Single Cell Transcriptomics |[Link](https://sib-swiss.github.io/single-cell-training)|2023 |3 days |scRNAseq, CITEseq, Multi modal Omics | |
|Introduction to single-cell RNA-seq data analysis |[Link](https://bioinformatics-core-shared-training.github.io/SingleCell_RNASeq_May23/)|2023 |3 days |scRNAseq | |
|10X Single Cell RNA-Seq Analysis |[Link](https://www.bioinformatics.babraham.ac.uk/training.html#10xrna)|2023 |1 day |scRNAseq | |
|Advanced Single-Cell RNAseq Data Analysis 2023 |[Link](https://www.earlham.ac.uk/events/advanced-single-cell-rnaseq-data-analysis-2023)|2023 |3 days |scRNAseq, CyTOF FACS | |
|Introduction to Single-Cell RNAseq |[Link](https://www.earlham.ac.uk/events/introduction-single-cell-rnaseq-2023)|2023 |4 days |scRNAseq | |
|Single Cell Genomics - Latin America and the Caribbean |[Link](https://coursesandconferences.wellcomeconnectingscience.org/event/single-cell-genomics-latin-america-and-the-caribbean-20230728/?utm_campaign=single-cell-genomics-2023-latin-america-and-the-caribbean&utm_medium=email&utm_source=dotdigital&utm_content=&utm_term=course&dm_i=6Y2C,DIQR,1ODY6K,1NJJM,1,)|2023 |5 days |scRNAseq | |
|Single Cell Technologies and Analysis |[Link](https://coursesandconferences.wellcomeconnectingscience.org/event/single-cell-technologies-and-analysis-20220715/)|2022 |5 days |scRNAseq, CyTOF FACS | |
|Single-Cell RNAseq Data Analysis 2022 |[Link](https://www.earlham.ac.uk/events/single-cell-rnaseq-data-analysis-2022)|2022 |4 days |scRNAseq | |
|Single-cell RNA-seq analysis using R |[Link](https://www.ebi.ac.uk/training/events/single-cell-rna-seq-analysis-using-r-2022/)|2022 |5 days |scRNAseq | |
|Single-cell RNA-seq analysis using Galaxy |[Link](https://www.ebi.ac.uk/training/events/single-cell-rna-seq-analysis-using-galaxy-0/)|2023 |5 days |scRNAseq | |
|Single cell RNA-seq analysis using Python |[Link](https://www.ebi.ac.uk/training/events/single-cell-rna-seq-analysis-2023/)|2023 |5 days |scRNAseq | |
|10X Single Cell RNA-Seq Analysis |[Link](https://wiki.illinois.edu/wiki/display/HPCBio/10X+Single+Cell+RNA-Seq+Analysis)|2019 |2 days |scRNAseq | |
|Single-cell RNA-seq data analysis workshop |[Link](https://hbctraining.github.io/scRNA-seq_online/)|2023 |3 days |scRNAseq | |
|Single Cell ATAC-Seq Data Analysis |[Link](https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki#atac-seq-analysis)|2023 |2 days |scRNAseq | |
|Introduction to Single-cell RNA-Seq Workshop |[Link](https://alexslemonade.github.io/2023-june-training/)|2023 |3 days |scRNAseq, CITEseq | |
|Advanced Single-cell Workshop |[Link](https://alexslemonade.github.io/2023-march-training/)|2023 |5 days |scRNAseq, CITEseq | |


</div>

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