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Published 20 hours ago • verified publisher icon theislab

Workflow and content updates in pathway enrichment chapter

Open soroorh opened this issue 2 years ago • 2 comments

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

soroorh avatar Dec 16 '22 06:12 soroorh

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?

PauBadiaM avatar Jan 10 '23 14:01 PauBadiaM

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.

soroorh avatar Jan 12 '23 17:01 soroorh