Abstract
Multimodal single-cell protein and transcriptomic profiling (e.g. CITE-seq) holds promise for comprehensive dissection of cellular heterogeneity, yet protein counts measured by oligo-conjugated-antibody can have substantial noise that masks biological variations. Here we integrated experiments and computational analysis to reveal two major noise sources: protein-specific noise from unbound antibodies and cell-specific noise captured by the shared variance of isotype controls and background protein counts. We provide an open source R package (dsb) to denoise and normalize CITE-seq data based on these findings. (https://cran.r-project.org/web/packages/dsb/index.html).
Competing Interest Statement
The authors have declared no competing interest.
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