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Add random and scSampler cell downsampling - #15

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JerryIshihara wants to merge 3 commits into
TrynkaLab:mainfrom
JerryIshihara:features/full-matrix-downsampling
Open

JerryIshihara wants to merge 3 commits into
TrynkaLab:mainfrom
JerryIshihara:features/full-matrix-downsampling

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@JerryIshihara

@JerryIshihara JerryIshihara commented Oct 14, 2026 •

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Summary

  • Add a sampling interface with random and scSampler methods, configurable fraction, number of draws, seed, and output prefix.
  • Reuse existing PCA or calculate a shared incremental PCA embedding for scSampler.
  • Save a shared HVG list for downstream prepare runs.
  • Export sampled H5AD files in chunks, preserving counts and annotations.
  • Record sampled cell indices and provenance in a manifest.

Roadmap

Refs JerryIshihara/sc-blipper#27 and JerryIshihara/sc-blipper#30.

Related workflow integration: JerryIshihara/sc-blipper#32 and TrynkaLab/sc-blipper#20.

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