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Bioconductor / OrchestratingSingleCellAnalysis

Content for the OSCA Book.
http://bioconductor.org/books/devel/OSCA/
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Include count-based dimensionality reduction options #30

Closed LTLA closed 4 years ago

LTLA commented 4 years ago

These would be appealing to avoid the mean-variance issues with the log-transformation prior to PCA.

Considering scry pending some improvements to efficiency (kstreet13/scry#7). I'd like to see that example get down to a minute's runtime so that the book chapter runs fairly quickly. Tagging @willtownes to keep track of this.

LTLA commented 4 years ago

May also put in the correspondence analysis from corral, tagging @laurenhsu1.

laurenhsu1 commented 4 years ago

That would be great! Is there already a section written about this, or should I draft/PR something?

LTLA commented 4 years ago

The relevant chapter would be reduced-dimensions.Rmd, but I was planning to just write that part myself. My understanding is that I can give corral a count matrix and it will give me a reduced dimensions; if that is correct, then the process should be simple enough. I do have some questions that I'll send to laurenhsu1/corral#2, though.