Single cell and spatial omics: A short introduction to the core concepts of scRNA-seq and more

[@sara_rojo]

I watched several videos trying to find an easy explanation about this. You made it so simple. Thank you. Best regards from México:)

[@larsjuhljensen]

Glad it was helpful!

[@geparada88]

Wow, such cutting-edge topics you are bringing to this channel. This is definitely one of my favorite areas of bioinformatics. There is so much more to say about scRNA-seq, but your video offers a nice and concise introduction. I very much agree that the sparsity of scRNA-seq data can be overcome by generating pseudo-bulks. In my case, I do clustering, followed by cell assignment and random pseudo-bulking. In this way, I artificially enhance the depth of my measuring units, while I can keep the cell type-specific information :)

[@larsjuhljensen]

Thanks a lot! What we're doing a lot is not to assign cell types, but rather to use variational autoencoders to compress the cells into a lower-dimensional latent space. It accomplishes much the same, since compressing the data into a lower-dimensional space inherently means that you are in some way averaging/summing up cells.

[@geparada88]

@@larsjuhljensen That sounds really interesting. I've been thinking along these lines too but in a less sophisticated way (just using knn to gather cells for pseudo-pooling across a lower dimensional space). I would need to learn about autoencoders to really understand your strategy, but I kind of get the point.

[@larsjuhljensen]

You can read about it on bioRxiv: doi.org/10.1101/2022.07.06.499022 Or you can watch Mikaela from my group explain it: kzbin.info/www/bejne/jqrJpH5qpNqdjMU

[@mohammadghorbani3003]

That was amazing sir. You teaching bioinformatics and sharing your knowledge of omics, is the best course that one can take.

Great introduction thank you.

[@larsjuhljensen]

You are welcome!

[@dannyjones7688]

Would be great if you could include figures and explain some more of the techniques, as people looking for youtube introductions rather than engaging with papers are less likely to understand some of these techniques! thanks :)

[@muhammadwaqasluqman2977]

wow, thank you so much.

[@larsjuhljensen]

You're welcome, I hope this short overview was useful!

[@pancake9191]

how am I supposed to understand without even one illustration picture

[@larsjuhljensen]

I would have loved to have good, simple graphical illustrations of the many different assays too, but the figures I could find were overly complicated and not suitable for a short overview presentation.