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CiteFuse enables multi-modal analysis of CITE-seq data
- Publication Year :
- 2019
- Publisher :
- Cold Spring Harbor Laboratory, 2019.
-
Abstract
- 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. Availability and implementation CiteFuse is freely available at http://shiny.maths.usyd.edu.au/CiteFuse/ as an online web service and at https://github.com/SydneyBioX/CiteFuse/ as an R package. Contact pengyi.yang@sydney.edu.au Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects :
- Statistics and Probability
Computer science
Modal analysis
Cell
Computational biology
Biochemistry
Epitope
Transcriptome
Epitopes
03 medical and health sciences
Software
0302 clinical medicine
medicine
Profiling (information science)
Cluster analysis
Molecular Biology
030304 developmental biology
0303 health sciences
Sequence Analysis, RNA
business.industry
Gene Expression Profiling
RNA
Computer Science Applications
Visualization
Computational Mathematics
medicine.anatomical_structure
Computational Theory and Mathematics
Protein Expression Analysis
Single-Cell Analysis
business
030217 neurology & neurosurgery
Subjects
Details
- Database :
- OpenAIRE
- Accession number :
- edsair.doi.dedup.....9e6603913113f0a400e5eb06764789fd