Seurat sctransform - does anyone know of a good explanation for biologists?

Question

[Lucy]

Hi,

I was wondering whether anyone knows of a good blog/video/post explaining sctransform in a clear and easy to understand way. I understand the idea of the approach but would like to further understand the details. The paper uses a lot of unfamiliar terms which makes it tricky to read.

Alternatively, if anyone wants to have a go at explaining it, I would much appreciate it!

Best wishes,

Lucy

Answer 1

[Thomas]

Florian Wagner has a great (and short) video explaining different scRNA-seq preprocessing methods here. The "the Pearson residuals from regularized negative binomial regression" approach implemented in scTransform is one of the approaches he explains in a very clear and understandable way.

Answer 2

[Vitis]

I found this document quite informative about the rationale and process of the transformation.

https://rawgit.com/ChristophH/sctransform/supp_html/supplement/variance_stabilizing_transformation.html