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index.qmd
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---
title: "SIB course Single Cell Transcriptomics"
---
::: {.callout-caution}
## Looking for previous material?
Are you looking for material of previous versions of the course? Find it at [sib-swiss.github.io/single-cell-training-archived](https://sib-swiss.github.io/single-cell-training-archived)
:::
<figure>
<img src="assets/images/umap_nonintegrated_dim50.png" width="500"/>
</figure>
## Teachers
- Luciano Cascione [ORCiD](https://orcid.org/0000-0002-4606-0637)
- Geert van Geest [ORCiD](https://orcid.org/0000-0002-1561-078X)
## Teachers of previous courses
- Tania Wyss [ORCiD](https://orcid.org/0000-0003-2641-0895)
- Rachel Marcone-Jeitziner [ORCiD](https://orcid.org/0000-0002-5711-8435)
- Alex Russell Lederer [ORCiD](https://orcid.org/0000-0001-6381-5088)
## Authors
- Tania Wyss [ORCiD](https://orcid.org/0000-0003-2641-0895)
- Rachel Marcone-Jeitziner [ORCiD](https://orcid.org/0000-0002-5711-8435)
- Alex Russell Lederer [ORCiD](https://orcid.org/0000-0001-6381-5088)
- Geert van Geest [ORCiD](https://orcid.org/0000-0002-1561-078X)
- Patricia Palagi [ORCiD](https://orcid.org/0000-0001-9062-6303)
## Attribution
Parts of this course are inspired by the [Broad Institute Single Cell Workshop](https://broadinstitute.github.io/2019_scWorkshop/index.html), the [CRUK CI Introduction to single-cell RNA-seq data analysis course](https://bioinformatics-core-shared-training.github.io/UnivCambridge_ScRnaSeq_Nov2021/) and courses previously developed by Walid Gharib at SIB.
## License & copyright
**License:** [CC BY 4.0](https://github.com/sib-swiss/single-cell-training/blob/master/LICENSE.md)
**Copyright:** [SIB Swiss Institute of Bioinformatics](https://www.sib.swiss/)
## Learning outcomes
### General learning outcomes
After this course, you will be able to:
- distinguish advantages and pitfalls of scRNAseq
- design your own scRNA-seq experiment
- apply a downstream analysis using R
### Learning outcomes explained
To reach the general learning outcomes above, we have set a number of smaller learning outcomes. Each chapter starts with these smaller learning outcomes. Use these at the start of a chapter to get an idea what you will learn. Use them also at the end of a chapter to evaluate whether you have learned what you were expected to learn.
## Learning experiences
To reach the learning outcomes we will use lectures, exercises, polls and group work. During exercises, you are free to discuss with other participants. During lectures, focus on the lecture only.
### Exercises
Each block has practical work involved. Some more than others. The practicals are subdivided into chapters, and we'll have a (short) discussion after each chapter. All answers to the practicals are incorporated, but they are hidden. Do the exercise first by yourself, before checking out the answer. If your answer is different from the answer in the practicals, try to figure out why they are different.