Cheat sheet(s) for advanced scRNA topics

[jashapiro]

We should create some cheat sheets for advanced Single Cell that include the functions that we use for cell typing, integration, and differential expression. We will also want to update the base scRNA cheatsheet with any additional functions that we are missing. I am thinking here partially of splitAltExps() which may have intro scRNA utility, but we don't really talk about much in the intro course (at this point).

[jaclyn-taroni]

Based on our experience last time – can we add converting from Seurat to SingleCellExperiment (with CITE-seq, ideally) even though we don't cover it during the course?

[jashapiro]

Based on our experience last time – can we add converting from Seurat to SingleCellExperiment (with CITE-seq, ideally) even though we don't cover it during the course?

Yes! When I started writing this issue, I was planning to include that, but by the time I actually was composing it slipped my mind!

[jaclyn-taroni]

:shrek:

[sjspielman]

Include Seurat conversion!

[sjspielman]

We will also want to update the base scRNA cheatsheet with any additional functions that we are missing.

The following are also missing from intro scRNA, so I will add these here (edit: here= in this PR, not to the advanced cheatsheet!) as well.

• scater::runUMAP()
• scater::runPCA()
• scater::plotReducedDim()
• scater::plotUMAP() (we don't actually run this function in the intro workshop but we tell them it's a shortcut in the exercises, so maybe this one belongs in both cheatsheets)

@jashapiro While writing this comment, I realize we may be on different pages for what counts as "intro" vs "advanced" - in my mind, splitAltExps belongs in the advanced cheatsheet because it's taught in the advanced workshop, but we may be circling back to that overall organization soon! So I would think something like that function should stay in advanced for now, but it might get moved in a forthcoming "swap scrnaseq workshop content" epic.

[jashapiro]

@jashapiro While writing this comment, I realize we may be on different pages for what counts as "intro" vs "advanced" - in my mind, splitAltExps belongs in the advanced cheatsheet because it's taught in the advanced workshop, but we may be circling back to that overall organization soon! So I would think something like that function should stay in advanced for now, but it might get moved in a forthcoming "swap scrnaseq workshop content" epic.

I don't think we are far apart. I think putting it in advanced for now is fine, but I can imagine it being useful for people in intro too, even if we haven't taught them yet. Ultimately, I think we may want to reorganize these by task rather than intro vs. advanced, but probably not for now.

[sjspielman]

Ultimately, I think we may want to reorganize these by task rather than intro vs. advanced, but probably not for now.

💯 agreed

Noting also a couple other functions to add over in intro (and in the future, probably into "what's in your SCE" topic) -

• assay()
• assayNames()
• reducedDim()
• reducedDimNames()