Live R Coding Session - Spatial transcriptomics data analysis with STdeconvolve and SpotClean

I record myself coding in the R programming language to perform an exploratory bioinformatics analysis of multi-cellular pixel resolution spatial transcriptomics Visium dataset from 10X Genomics using STdeconvolve with SpotClean preprocessing. I hope this will help give students a sense for how I would go about doing an exploratory bioinformatics data analysis, the kinds of challenges I often face and how I try to address them, and the types of 'sanity checks' I like to perform along the way.
Some potentially helpful moments:
- bypassing R version requirements when installing R packages: • Live R Coding Session ...
- running spot decontamination preprocessing with SpotClean: • Live R Coding Session ...
- running cell-type deconvolution with STdeconvolve: • Live R Coding Session ...
- debugging when the data does not look how you expect: • Live R Coding Session ...
- tuning STdeconvolve cleanCounts() parameters: • Live R Coding Session ...
- evaluating SpotClean results: • Live R Coding Session ...
- running STdeconvolve with output from SpotClean: • Live R Coding Session ...
- tuning STdeconvolve visualization parameters: • Live R Coding Session ...
- comparing STdeconvolve results with and without SpotClean preprocessing: • Live R Coding Session ...
- committing to Github: • Live R Coding Session ...
To try it out for yourself, check out:
- Code from this coding session: github.com/JEFworks/coding_vi...
- STdeconvolve: jef.works/STdeconvolve/
- SpotClean: github.com/zijianni/SpotClean
Please take my live commentary with a grain of salt ;) Here are some minor mistakes I've caught in the video:
- the scaling factor converts into units of pixels, not microns

[@user-kq5sk6mf4d]

Omg thank you Prof Jean Fan. As a student self learning bioinformatics for my research, I have really learnt a lot from watching your video as you work through the data with full details on how to troubleshoot etc. I hope you continue making live sessions!

[@hswigg]

these types of raw videos with live debugging is super helpful. Thank you so much!

[@nermeenabdelmoez6347]

I hope you make more videos, Thanks and keep going 🍀🙏

[@haohuifang8674]

Great tutorial type lectures. Hope to learn more from you. Have subscribed to you for a while. Really useful!

[@Brickkzz]

Having a video like this but in Python would be great!

[@mohadesehzaree4918]

Thank you Prof. Fan. I got the below error when tried to run "decont_obj

[@AA-md7bt]

Disappointing!!