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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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Add bulk metadata file to download section #56

Closed allyhawkins closed 2 years ago

allyhawkins commented 2 years ago

Closes #55. Here I am adding in a short section on the bulk_metadata.tsv file that is included in downloads for projects with bulk RNA-sequencing. I chose to just add one sentence about the metadata file instead of going into detail about every single-column because I wasn't quite sure we needed that level of detail. If others feel differently then I'm happy to add in a table to the section on metadata at the bottom of the page with the details for each column.

Based on what we add here, I also wanted to make the associated changes for https://github.com/AlexsLemonade/scpca-portal/issues/144, copying over the section we have here about if a project contains bulk files. Based on any wording changes that may be made here, I will then make the necessary changes to address https://github.com/AlexsLemonade/scpca-portal/issues/144 so we don't have to open PR's with similar wording.

allyhawkins commented 2 years ago

@jashapiro I believe this is ready for another look. I went ahead and updated the file names and will then file an issue to update the screenshots with the new file names.

I also tried something with the metadata explanation where I'm linking out to the descriptions of the metadata that is actually in the SCE object, since much of that metadata is getting pulled into the single_cell_metadata.tsv. I started to add it to the existing table, but much of it is repeated there so it seemed redundant.

I then added a sentence about the bulk metadata containing all of the processing related metadata and none of the disease specific metadata, noting the columns that are removed. Let me know if this is not clear to you and if you would prefer a different approach.

allyhawkins commented 2 years ago

I incorporated your suggestions @jashapiro and went ahead and reorganized the section slightly so that the beginning explains all files that are included in either type of download and then we show the screenshots that display the differences in downloading by project and by sample. Was this what you were thinking in https://github.com/AlexsLemonade/scpca-docs/pull/56#discussion_r817806138.

I also filed #57 to update the screenshots so we can wait to merge this until the screenshots are integrated.