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

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

Рет қаралды 7,373

Lars Juhl Jensen

Күн бұрын

Пікірлер: 13

@sara_rojo 6 ай бұрын

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

@larsjuhljensen 6 ай бұрын

Glad it was helpful!

@geparada88 Жыл бұрын

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 Жыл бұрын

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 Жыл бұрын

@@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 Жыл бұрын

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: kzfaq.info/get/bejne/jt-Wpq5l1NvOhpc.html

@mohammadghorbani3003 Жыл бұрын

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

8 ай бұрын

Great introduction thank you.

@larsjuhljensen 8 ай бұрын

You are welcome!

@muhammadwaqasluqman2977 6 ай бұрын

wow, thank you so much.

@larsjuhljensen 6 ай бұрын

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

@pancake9191 9 ай бұрын

how am I supposed to understand without even one illustration picture

@larsjuhljensen 9 ай бұрын

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.