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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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Getting started section for multiplexed samples #85

Closed allyhawkins closed 2 years ago

allyhawkins commented 2 years ago

Closes #74. ⚠️ Stacked on #83 ⚠️

Here I added a section to the Getting started with an ScPCA dataset that includes special considerations for multiplexed samples. I was unsure about the level of detail that we wanted, but based on the two points described in #74, I was sure to include a description of what a multiplex sample is and information on how to filter to the sample of interest.

I also included a statement about how the initial analysis that is described in the beginning of the getting started section for single sample libraries - filtering, normalization, dimensionality reduction - can be performed as usual. Then I included some details about demultiplexing and identifying which cells belong to which samples, explaining that those results are already summarized and providing a link to the SCE file contents page. I then have a chunk of code showing an example of separating by sample into a new object for downstream analysis. Is there anything from this that is missing or not detailed enough?

The last little bit I included was a few external resources for people to use based on the types of demultiplexing that we include. In this PR I'm also adding in the link to this section in the FAQ: What is a multiplexed sample.

Again, I wasn't 100 percent sure on detail and structure here so if there was something else that others had in mind, I am definitely open to it.

allyhawkins commented 2 years ago

Thanks for the review @jashapiro. I incorporated your comments and then specified the actual column names where the results are stored per your comment. Let me know if there is anything else that should be addressed.