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scGPT integration-based label transfer #981

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@dorien-er

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@dorien-er

workflows/annotation/scgpt_integration_knn was deprecated in OP 2.1.0 because:

  • zero-shot models are trained on gene names
  • gene names are not unique, causing issues when the query and reference dataset are concatenated
  • current sanitation of --var_gene_name params is tailored towards ensembl id sanitation, but results in faulty behavior when gene names are provided

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