Droplet scRNA-seq is not zero-inflated

By Valentine Svensson. Nature Biotechnology, 2019

311 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/a2c2403d208f36d32363b11329250fd390d952d5

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In Molecular Biology

Citations in the corpus

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models (2019, unknown): “To explore this, we use a pair of datasets that provides a snap-shot of hematopoiesis in mice [HEMATO-Tusi (Tusi et al , 2018) Notably, the HEMATO-Tusi dataset contains cells that appear to be more terminally differentiated, which are located at the extremes of the two primary branches.”
Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients (2020, background): “However, recent studies suggested that those models are too complex and introduce artiﬁcial complexity (Silverman et al., 2018; Svensson, 2020; Townes et al., 2019).”
Aitchison’s Compositional Data Analysis 40 Years on: A Reappraisal (2022, background): “There are currently no generally accepted standards for handling zeros [93].”
Joint probabilistic modeling of single-cell multi-omic data with totalVI (2021, background): “The negative binomial distribution has been shown to adequately handle the limited sensitivity and over-dispersion that are characteristic of this data [61].”
Comparison and evaluation of statistical error models for scRNA-seq (2021, methodology): “Availability of data andmaterials The technical control datasets [8, 14], ChromiumV3 NIH3T3 cell line dataset and ChromiumV3 PBMC dataset [74] used in the main text are available publically from CaltechDATA repository record 1264 [75].”
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues (2020, unknown): “Taken together, the results of this power analysis are in agreement with other efforts tomodel biological and technical sources of zero-inflation within scRNA-seq data (e.g., https://satijalab.org/howmanycells and Kharchenko et al., 2014; Svensson, 2020).”
Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model (2019, background): “This also demonstrates that UMI counts are not zero inflated , consistent with [29].”
Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender (2019, background): “By default, the network has two hidden layers [100, 50].”