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Decoupler pathway inference: consider gene symbol field in AnnData #327

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pcm32 opened this issue Jul 25, 2024 · 0 comments
Open

Decoupler pathway inference: consider gene symbol field in AnnData #327

pcm32 opened this issue Jul 25, 2024 · 0 comments
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persist-seq Requests from Persist-Seq

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pcm32 commented Jul 25, 2024

Often we provide to these tools AnnData files where the index is the gene_id and the gene symbols are in another field of the var. However, gene set tools will often rely on the gene symbol, so we need to indicate where the gene symbol is in our anndata and make use of this information so that the tool runs against those gene symbols. This is done in decoupler AUCell here:

https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/blob/main/tools/tertiary-analysis/decoupler/decoupler_aucell_score.py#L117

@pcm32 pcm32 added the persist-seq Requests from Persist-Seq label Jul 25, 2024
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