CellBender – unsupervised removal of systematic background noise from droplet-based single-cell experiments

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Droplet-based single-cell assays, including single-cell RNA sequencing (scRNA-seq), single-nucleus RNA sequencing (snRNA-seq) and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), generate considerable background noise counts, the hallmark of which is nonzero counts in cell-free droplets and off-target gene expression in unexpected cell types. Such systematic background noise can lead to batch effects and spurious differential gene expression results.

Researchers from the Broad Institute of MIT and Harvard have developed a deep generative model based on the phenomenology of noise generation in droplet-based assays. The proposed model accurately distinguishes cell-containing droplets from cell-free droplets, learns the background noise profile and provides noise-free quantification in an end-to-end fashion. The researchers implement this approach in the scalable and robust open-source software package CellBender. Analysis of simulated data demonstrates that CellBender operates near the theoretically optimal denoising limit. Extensive evaluations using real datasets and experimental benchmarks highlight enhanced concordance between droplet-based single-cell data and established gene expression patterns, while the learned background noise profile provides evidence of degraded or uncaptured cell types.

The CellBender model

Extended Data Fig. 1

(a) The CellBender generative model for noisy single-cell count data. (b) The variational posterior used by CellBender. The neural network NNenc takes the observed data as input and yields the parameters of various variational distributions assumed for the local latent variables. The global latent variables are treated in the usual mean-field approximation.

Availability – CellBender can be obtained from https://github.com/broadinstitute/CellBender.

Fleming SJ, Chaffin MD, Arduini A, Akkad AD, Banks E, Marioni JC, Philippakis AA, Ellinor PT, Babadi M. (2023) Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender. Nat Methods [Epub ahead of print]. [abstract]