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AlexsLemonade / scpca-docs

User information about ScPCA processing
https://scpca.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Update docs to note we always use spliced and unspliced cDNA #174

Closed allyhawkins closed 11 months ago

allyhawkins commented 11 months ago

Closes #142 Note that this PR is getting merged into the new documentation-improvements branch that I made. This branch is protected and should be use for making all the pre-AnnData and pre-celltype changes.

Here I updated the section on post processing alevin-fry to indicate that we always combine counts. I also added a sentence to the sce file contents to note that the counts matrix includes the counts from both spliced and unspliced cDNA and included a link to the processing information.

I did include a sentence about the presence of the spliced assay in the object, but I'm unsure if we want to mention that or not... I'm curious about what others think.

jaclyn-taroni commented 11 months ago

Now that we want to cut an initial release after this goes in, do we want to change the base branch to main @allyhawkins ?

allyhawkins commented 11 months ago

Now that we want to cut an initial release after this goes in, do we want to change the base branch to main @allyhawkins ?

Yes, I think that will be easier. I'll do that.