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hbctraining / scRNA-seq_online

https://hbctraining.github.io/scRNA-seq_online/.
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new version of scTransform released! #78

Closed pipes82 closed 1 year ago

pipes82 commented 2 years ago

Hey All! Let me know if I am issuing too many issues - or better to post in Slack? Feel free to close if not interested in updating right now. I am currently testing it out so feel free to reach out too - supposed to be better memory/resource usage.

Vignette: https://satijalab.org/seurat/articles/sctransform_v2_vignette.html Corresponding paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02584-9

I had to update all of the Seurat dependencies before installing:

remotes::install_github("mojaveazure/seurat-object")
devtools::install_github("satijalab/sctransform", ref = "develop")
devtools::install_github("satijalab/seurat", ref = "develop")
BiocManager::install("glmGamPoi")

Best, Mary

mistrm82 commented 2 years ago

Thanks @pipes82 :) We'll probably address this closer to the next workshop.

Preference for GitHub issues, that way we remember to address it!

mistrm82 commented 1 year ago

Check to see if we still need the dev branch

mistrm82 commented 1 year ago

Don't need the dev branch, only need to make sure people have glmGamPoi installed (which is on our prep list anayways)