Seurat SingleR

The software tool 'Seurat SingleR' evaluates ten cell-type annotation methods for single-cell RNA-Seq (scRNA-Seq) data analysis, providing a comprehensive comparison. The methods, available as R packages, include those specifically designed for single cell research (Seurat, scmap, SingleR, CHETAH, SingleCellNet, scID, Garnett, SCINA) and those repurposed from deconvoluting DNA methylation data (Linear Constrained Projection - CP and Robust Partial Correlations - RPC). Systematic comparisons using various scRNA-seq datasets and simulation data assess accuracy, robustness, and capabilities for rare and unknown cell-type detection.

Topic

RNA-Seq;Cell biology;Transcriptomics

Detail

  • Operation: Standardisation and normalisation;Deisotoping;Regression analysis

  • Software interface: Command-line user interface

  • Language: R

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: NIEHS through funds provided by the trans-NIH Big Data to Knowledge (BD2K) initiative (www.bd2k.nih.gov) NLM, awarded by NICHD.

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  • Output: -

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  • Collection: -

  • Maturity: -

Publications

  • Evaluation of Cell Type Annotation R Packages on Single Cell RNA-seq Data
  • Huang, Q.; Liu, Y.; Du, Y.; Garmire, L. Evaluation of Cell Type Annotation R Packages on Single Cell RNA-seq Data. bioRxiv 2020. doi: 10.1101/827139
  • https://doi.org/10.1101/827139
  • PMID: -
  • PMC: -

Download and documentation

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