ArticleGenome biology2024
scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Article
- Systematic benchmarking of ambient RNA decontamination tools to advance precision in single-cell transcriptomic analysis.Nature communications · 2026Article
- Early cell-autonomous and niche-mediated epithelial response to influenza infection in primary alveolar organoids.JCI insight · 2026Article
- Analytical Methods and Application of Single-Cell and Single-Nucleus Transcriptomics in the Study of Ischemic Stroke.Biomolecules · 2026Review
- DeSpotX: Identifiability-Based Decontamination for Spatial Transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- The changing landscape of gene expression analysis.Briefings in bioinformatics · 2026Review
- Optimized Method for High-Quality Isolation of Single-Nuclei From Mosquito Fat Body for RNA Sequencing.Bio-protocol · 2026Article
- Macrophage-derived CCL20 promotes abdominal aortic aneurysm progression via lymphocytes CCR6.Frontiers in immunology · 2026Article
- Multi-omics and experimental validation identify USP54 as a prognostic deubiquitinase promoting pancreatic ductal adenocarcinoma progression within the immune microenvironment.Frontiers in immunology · 2026Article
- Benchmarking computational decontamination of ambient RNA.Frontiers in bioinformatics · 2026Article
- Early cell autonomous and niche-mediated alveolar epithelial response to influenza infection in primary lung organoids.bioRxiv : the preprint server for biology · 2025Article
- Cluster-independent multiscale marker identification in single-cell RNA-seq data using localized marker detector (LMD).Communications biology · 2025Article
- Benchmarking of computational demultiplexing methods for single-nucleus RNA sequencing data.Briefings in bioinformatics · 2025Article
- scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data.Genome biology · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
In droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules biases the quantification of gene expression levels. Existing methods correct the contamination for all genes globally. However, there lacks specific evaluation of correction efficacy for varying contamination levels. Here, we show that DecontX and CellBender under-correct highly contaminating genes, while SoupX and scAR over-correct lowly/non-contaminating genes. Here, we develop scCDC as the first method to detect the contamination-causing genes and only correct expression levels of these genes, some of which are cell-type markers. Compared with existing decontamination methods, scCDC excels in decontaminating highly contaminating genes while avoiding over-correction of other genes.
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