Leveraging Machine Learning for Robust Cell Type Annotation: A Data-Driven Perspective

Key Highlights

  • Cell-type annotation of scRNA-seq data is a complex data-driven process that can be impacted by user bias. Reliable cell-type annotation is crucial, and we at Elucidata have been actively working towards building high-quality pipelines to accurately and reproducibly annotate cell types.
  • When compared to author-assigned annotations, automated methods for cell-type identification in scRNA-seq data show limited agreement, indicating substantial variability in published cell annotations.
  • The choice of reference data has a more pronounced impact on computational cell-type predictions than the specific algorithm employed, underscoring the data-centric nature of this problem.
  • The whitepaper explores available cell-type annotation methods, shares the results of an extensive in-house benchmarking study, and introduces Elucidata's approach to improving quality and reproducibility.

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