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treekoR: identifying cellular-to-phenotype associations by elucidating hierarchical relationships in high-dimensional cytometry data.

Adam ChanWei JiangEmily BlythJean YangEllis Patrick
Published in: Genome biology (2021)
High-throughput single-cell technologies hold the promise of discovering novel cellular relationships with disease. However, analytical workflows constructed for these technologies to associate cell proportions with disease often employ unsupervised clustering techniques that overlook the valuable hierarchical structures that have been used to define cell types. We present treekoR, a framework that empirically recapitulates these structures, facilitating multiple quantifications and comparisons of cell type proportions. Our results from twelve case studies reinforce the importance of quantifying proportions relative to parent populations in the analyses of cytometry data - as failing to do so can lead to missing important biological insights.
Keyphrases
  • single cell
  • high throughput
  • rna seq
  • big data
  • electronic health record
  • high resolution
  • machine learning
  • cell therapy
  • mass spectrometry
  • artificial intelligence
  • bone marrow
  • genetic diversity