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  "Title": "Cepo for the identification of differentially stable genes",
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  "Description": "Defining the identity of a cell is fundamental to\nunderstand the heterogeneity of cells to various environmental\nsignals and perturbations. We present Cepo, a new method to\nexplore cell identities from single-cell RNA-sequencing data\nusing differential stability as a new metric to define cell\nidentity genes. Cepo computes cell-type specific gene\nstatistics pertaining to differential stable gene expression.",
  "License": "MIT + file LICENSE",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:57:21 UTC",
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