Journal
BIOINFORMATICS
Volume 36, Issue 14, Pages 4137-4143Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btaa282
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Funding
- Australian Research Council (ARC)/Discovery Early Career Researcher Award (DECRA) [DE170100759]
- National Health and Medical Research Council (NHMRC) [1173469]
- NHMRC [1111338]
- ARC [DP170100654]
- Research Training Program (RTP)
- Chen Family Research Scholarship
- ARC
- Children's Medical Research Institute
- National Health and Medical Research Council of Australia [1111338, 1173469] Funding Source: NHMRC
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Motivation: Multi-modal profiling of single cells represents one of the latest technological advancements in molecular biology. Among various single-cell multi-modal strategies, cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) allows simultaneous quantification of two distinct species: RNA and cell-surface proteins. Here, we introduce CiteFuse, a streamlined package consisting of a suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data. Results: We demonstrate the capacity of CiteFuse to integrate the two data modalities and its relative advantage against data generated from single-modality profiling using both simulations and real-world CITE-seq data. Furthermore, we illustrate a novel doublet detection method based on a combined index of cell hashing and transcriptome data. Finally, we demonstrate CiteFuse for predicting ligand-receptor interactions by using multi-modal CITE-seq data. Collectively, we demonstrate the utility and effectiveness of CiteFuse for the integrative analysis of transcriptome and epitope profiles from CITE-seq data.
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