Workflow and content updates in pathway enrichment chapter

theislab / single-cell-best-practices

https://www.sc-best-practices.org

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Workflow and content updates in pathway enrichment chapter #132

Open soroorh opened 1 year ago

soroorh commented 1 year ago

Suggestions and plans follow-ups to #119

Replace pseudo-replicate-based workflow for pseudobulking to sample-based workflow
Use a more informative contrast for between-cell type gene set enrichment in the limma-fry
Consider including functional analysis (TF footprint enrichment) and discussion on methods of enrichment analysis that account for the weights in the prior knowledge for the estimation of scores

PauBadiaM commented 1 year ago

Hi @soroorh,

Like I mentioned in #119, I would interested in contributing to this section update. Is someone already actively working on this? Now that I'm back from holidays I could start working on this and open a PR, is that okay?

soroorh commented 1 year ago

Hi @PauBadiaM, Happy 2023 and thanks for your interest in contributing to the chapter. Please do consider opening a PR relating to the 3rd bullet point. Happy to consider your suggestions. Thanks.