10x Visium spatial transcriptomics data analysis with STdeconvolve in R

I'm trying out different video styles to teach students about bioinformatics analyses for spatially resolved transcriptomics data. In previous videos, I recorded myself live-coding and narrating through all my thought processes, mistakes, and troubleshooting. Now, I'm trying out sped-up versions.
So in this video, I speed through coding a bioinformatics analysis in the R programming language to characterize how cell-types are organized in a breast cancer tissue section profiled by the 10X Visium spatial transcriptomics technology (www.10xgenomic...) using our reference-free deconvolution analysis tool STdeconvolve (www.nature.com...)
Particularly since we have a highschool student interning with us this summer who will be applying STdeconvolve to some new spatial transcriptomics data, I hope this video will be a useful educational resource.
See our lab blog for the code from this session to try it out for yourself:
jef.works/blog...
Some potentially helpful moments:
- introduction/background: • 10x Visium spatial tra...
- sped-up coding: • 10x Visium spatial tra...
- result summary: • 10x Visium spatial tra...
- lab mascot Remy makes a surprise appearance: • 10x Visium spatial tra...
Music by Stockaudios (pixabay.com/us...)

[@juliangrandvallet5359]

Thank you, Dr., Please keep doing these videos! they are very helpful

[@taobohu1402]

Hi Prof. Fan, thank you so much, very nice tools! And very cute dog :)

[@izabela8725]

great videos, very helpful! Will you by any chance also analyse Xenium spatial transcriptomics data from 10X?

[@0jaxay0]

nice

[@relaxenjoy9817]

Thank you
Does it mean, that if one is using SpaceRanger v2 to process the sequencing Visium data, using STdeconvolve in R is unnesecary afterwards?
best