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CellBender removes technical artifacts from single-cell RNA sequencing data

The conversion of biological molecules into digital signals through sequencing is a complex process that often generates substantial systematic background noise. This noise can obscure important biological insights. However, by precisely identifying and removing this noise, we can bring the true signal into focus and eliminate misleading results from downstream analyses.

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Fig. 1: The effect of CellBender noise removal on RNA sequencing data.

References

  1. Aldridge, S. & Teichmann, S. A. Single cell transcriptomics comes of age. Nat. Commun. 11, 4307 (2020). This review article presents an overview of the past decade of technological advances in single-cell RNA sequencing.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Kingma, D. P. & Welling, M. Auto-encoding variational Bayes. Preprint at https://doi.org/10.48550/arXiv.1312.6114 (2013). This preprint establishes the foundations for the use of stochastic variational inference in amortized Bayesian models using modern gradient-based optimization techniques.

  3. Bingham, E. et al. Pyro: deep universal probabilistic programming. J. Machine Learning Res. 20, 1–6 (2019). This paper establishes a general programming language to facilitate stochastic variational inference in Bayesian models using modern gradient-based optimization techniques.

    Google Scholar 

  4. Stoeckius, M. et al. Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865–868 (2017). This paper introduces CITE-seq, a technique for quantifying antibody-labeled proteins along with RNA in single-cell experiments.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Chen, X. et al. A rapid and robust method for single cell chromatin accessibility profiling. Nat. Commun. 9, 5345 (2018). This paper introduces the single-cell version of ATAC-seq, enabling chromatin accessibility measurements.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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This is a summary of: Fleming, S. J. et al. Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender. Nat. Methods https://doi.org/10.1038/s41592-023-01943-7 (2023).

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CellBender removes technical artifacts from single-cell RNA sequencing data. Nat Methods 20, 1285–1286 (2023). https://doi.org/10.1038/s41592-023-01946-4

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