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hbctraining / scRNA-seq_online

https://hbctraining.github.io/scRNA-seq_online/.
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cell cycle scoring may need updates #107

Closed hwick closed 11 months ago

hwick commented 1 year ago

The resources on cell cycle scoring might need some updating -consider adding required libraries (rCurl, AnnotationHub, ensembldb) -object seurat_control doesn't appear in materials linking to the page (page is currently linked from 06_SC_SCT_normalization -skips normalization step which appears on the SC_SCT_normalization page -RunPCA step throws an error (consider adding FindVariableFeatures step which is mentioned on the SC_SCT_normalization page):


Error in PrepDR(object = object, features = features, verbose = verbose) : 
Variable features haven't been set. Run FindVariableFeatures() or provide a vector of feature names.
hwick commented 1 year ago

I have added the libraries and changed seurat_control to seurat_phase, but ended up not adding the normalization step since it mentions "PCA is run only using the most variable features identified previously."

mistrm82 commented 11 months ago

thanks @hwick ! I ended up adding FindVariableFeatures() and just a note to not run it if you had previously. I think we're all set here!