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Overview

  • Introduces the feature to specify expected doublet rates on a per-sample basis for doublet detection using scrublet for heterogeneous datasets.
  • Enables configuration through a CSV file mapping sample identifiers to their expected doublet rates.
  • Maintains fallback to a global default rate if per-sample data is unavailable or missing for a sample.

Motivation

This update addresses the limitations of a single expected doublet rate by allowing tailored configurations, which can enhance doublet predictions when sample-specific rates are known or required.

Details

  • Updates configuration options to allow toggling per-sample rate usage and specifying the CSV file path.
  • Modifies pipeline logic to read sample-specific rates from the CSV file and revert to the default as necessary.
  • Adds a resource CSV example for user reference.

@AhmadAlalti AhmadAlalti added the enhancement New feature or request label Nov 7, 2025
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@deevdevil88 deevdevil88 left a comment

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i have chatted with Ahmad, and he has tested extensively that this works

@deevdevil88 deevdevil88 merged commit 81721cf into DendrouLab:main Dec 11, 2025
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2 participants