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CiteFuse enables multi-modal analysis of CITE-seq data.

Hani Jieun Kim1,2,3, Yingxin Lin1,2, Thomas A Geddes2,4

  • 1School of Mathematics and Statistics, Faculty of Science, The University of Sydney, Sydney 2006, Australia.

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Summary
This summary is machine-generated.

CiteFuse is a new R package that streamlines multi-modal single-cell analysis using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq). It offers tools for doublet detection, data integration, and visualization, enhancing RNA and protein expression analysis.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Single-cell multi-modal profiling is an emerging technology.
  • Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) enables simultaneous RNA and cell-surface protein quantification.

Purpose of the Study:

  • Introduce CiteFuse, a comprehensive R package for CITE-seq data analysis.
  • Provide tools for doublet detection, modality integration, and differential expression analysis.
  • Facilitate ligand-receptor interaction analysis and interactive visualization of CITE-seq data.

Main Methods:

  • Development of a streamlined R package, CiteFuse.
  • Implementation of a novel doublet detection method combining cell hashing and transcriptome data.
  • Utilizing simulations and real-world CITE-seq data to demonstrate CiteFuse's capabilities.

Main Results:

  • CiteFuse effectively integrates RNA and protein data from CITE-seq.
  • The package demonstrates advantages over single-modality profiling.
  • CiteFuse successfully predicts ligand-receptor interactions using multi-modal data.

Conclusions:

  • CiteFuse is a valuable tool for the integrative analysis of CITE-seq data.
  • The package enhances the utility of multi-modal single-cell profiling.
  • CiteFuse is available as a web service and an R package.