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scEiaD

Harmonize all publicly available scRNA-seq datasets for retina

Numbers

  • 33 datasets
  • 3 species (human, mouse, macaque)
  • 1.2e6 cells go in, 7.7e5 come out
  • 30 different cell types

Methods

  • Curate data, curate cell type labels
  • Re-process all with kallisto-bustools
  • Grid search and scPOP to ID best integration method (winner: scVI)
  • Grid search again with scVI only to ID best params (5000 HVG, 8 latent dims)
    • Build scVI model on human data, then use scVI/scArches query mode to add mouse and macaque data.
  • UMAP
  • xgboost cell type prediction to label unlabelled cells

Data

How do I add my own data to scEiaD?

It is possible! Even better, you don't have to ask me! Or tell me!

Interactive colab notebook

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Snakefile-based process to turn 1.4 million ocular cells into a unified meta-atlas

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