Future idea: Use SingleR with SCPCL000822 and SCPCL000824 as references to annotate remaining Ewing samples

[allyhawkins]

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#292

Describe the goals of the changes to the analysis module.

I noticed that when using all tumor cells as a reference and celldex references with SingleR we get a lot of cells that are tumor cells that have lower expression of marker genes than I would naively expect. I think it's likely that some cells will be more similar to cells from other Ewing samples than to normal cell types in the celldex reference, resulting in more cells being called tumor than actually should be.

One thought I had is to create a reference using the two samples that have a good mix of tumor/normal cells in them (SCPCL000822 and SCPCL000824) and use those as a reference with celldex to annotate the rest of the samples in the project.

What will your pull request contain?

This will probably be at least 2 PRs that will do the following:

• Generate a reference using the annotations from 822 and 824.
• Create a workflow that uses that reference and the 04-run-singler.R script to run SingleR for all other samples in the project. This workflow could probably also use the same template report 02-singler-results.Rmd to evaluate the results.

Will you require additional software beyond what is already in the analysis module?

No

Will you require different computational resources beyond what the analysis module already uses?

No

If known, when do you expect to file the pull request?

We should do this once we have confidently annotated normal cells in 822 and 824. I also don't know that we need to do this, but I think it could be helpful in refining the annotations that we currently have so I'm filing this as an idea for future analysis.