Results section - Additional Modalities

[allyhawkins]

Closes #28
Stacked on #34

This PR adds a section to the results covering additional modalities. I left one question as an html comment about how detailed we want to be with genetic demultiplexing. I gave an overview of the process, but didn't mention each individual tool that is used. We will definitely mention all of the individual tools used in the methods, but do we want to be more detailed here and include them in the text?

The sections on bulk and spatial are pretty simple, but are there additional details I should include?

[jaclyn-taroni]

I started editing this in jaclyn-taroni/37-review-additional-modalities but decided it makes sense to have you look through #47, which includes a decent amount of reorganization, and/or resolve #34. Then, we should mirror how we talk about inputs/outputs/etc. there in this section.

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[allyhawkins]

Okay I did quite a bit of reorganizing and rewriting for this section to try and follow how we talk about the main workflow. This should now be ready for @jaclyn-taroni to take a look.

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[allyhawkins]

I've updated this to include the edits from both stacked PRs and filled in the TODOs.

• For the ADT normalization citation, there isn't really a paper that I could find, but I used the OSCA section as the reference? That's what we link in our docs and there's no references there either.
• For the demultiplexing citations, there's a paper that explains demultiplexing with Seurat, but not one for DropletUtils.

I believe I got all the other ones and this should be ready for another look @jaclyn-taroni.

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[jaclyn-taroni]

When in doubt, you can use the DOI of the Bioconductor package.

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