ArticleGenome biology2021
DropletQC: improved identification of empty droplets and damaged cells in single-cell RNA-seq data.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Leveraging Single-Cell RNA Sequencing to Characterize Murine Ewing Sarcoma Xenografts.Methods in molecular biology (Clifton, N.J.) · 2027Article
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- Supporting-like cells constitute an alternative steroidogenic lineage conserved in amniotes.bioRxiv : the preprint server for biology · 2026Article
- Emergent latent neurotoxic effects of manganese following nominal chronic exposures in human stem cell and Caenorhabditis elegans models.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
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- Single-cell lung eQTL dataset of Asian never-smokers highlights the roles of alveolar cells in lung cancer etiology.bioRxiv : the preprint server for biology · 2026Article
- Developmental determinants of male bias in medulloblastoma.bioRxiv : the preprint server for biology · 2026Article
- CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease.Nature neuroscience · 2026Article
- Flexibility of cell fates and functions across sex determination systems revealed by comparative single-cell analyses.bioRxiv : the preprint server for biology · 2026Article
- Leveraging Single-Cell Technologies to Advance Understanding of Myocardial Disease.Circulation research · 2026Review
- PITX2 dosage-dependent changes in pacemaker cell state underlie sinus node dysfunction and atrial arrhythmias.Nature communications · 2025Article
- Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex.Cell reports · 2025Article
- Remodeling of the immune microenvironment is linked to adverse outcome in pediatric T cell acute lymphoblastic leukemia.Nature communications · 2025Article
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- Divergent accumulation patterns of SNVs and INDELs reveal negative selection in noncancerous cells.Innovation (Cambridge (Mass.)) · 2025Article
- Comparison of single-cell long-read and short-read transcriptome sequencing via cDNA molecule matching: quality evaluation of the MAS-ISO-seq approach.NAR genomics and bioinformatics · 2025Article
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2 authors.
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Abstract
backgroundAdvances in droplet-based single-cell RNA-sequencing (scRNA-seq) have dramatically increased throughput, allowing tens of thousands of cells to be routinely sequenced in a single experiment. In addition to cells, droplets capture cell-free "ambient" RNA predominantly caused by lysis of cells during sample preparation. Samples with high ambient RNA concentration can create challenges in accurately distinguishing cell-containing droplets and droplets containing ambient RNA. Current methods to separate these groups often retain a significant number of droplets that do not contain cells or empty droplets. Additionally, there are currently no methods available to detect droplets containing damaged cells, which comprise partially lysed cells, the original source of the ambient RNA.
resultsHere, we describe DropletQC, a new method that is able to detect empty droplets, damaged, and intact cells, and accurately distinguish them from one another. This approach is based on a novel quality control metric, the nuclear fraction, which quantifies for each droplet the fraction of RNA originating from unspliced, nuclear pre-mRNA. We demonstrate how DropletQC provides a powerful extension to existing computational methods for identifying empty droplets such as EmptyDrops.
conclusionsWe implement DropletQC as an R package, which can be easily integrated into existing single-cell analysis workflows.
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