DoubletFinder
An R package that predicts doublets (multiple cells mistaken as one) in single-cell RNA sequencing data using artificial nearest neighbor analysis.
What is DoubletFinder?
DoubletFinder is an R package that detects doublets—technical artifacts where multiple cells are incorrectly identified as a single cell—in single-cell RNA sequencing data. It solves the problem of data contamination by identifying and removing these doublets, which is critical for accurate clustering, differential expression analysis, and biological interpretation. The package uses a strategy of generating artificial doublets and analyzing k-nearest neighbor proportions in PCA space to predict real doublets in the dataset.
Bioinformaticians, computational biologists, and researchers analyzing single-cell RNA sequencing data who use the Seurat toolkit in R and need to ensure high data quality by removing technical artifacts.
Developers choose DoubletFinder for its robust, dataset-specific parameter optimization via BCmvn, its seamless integration with Seurat workflows, and its ability to adjust for homotypic doublets, leading to more accurate and interpretable single-cell analyses compared to generic thresholding methods.
Overview
R package for detecting doublets in single-cell RNA sequencing data
Use Cases
Best For
- Identifying heterotypic doublets in 10x Genomics scRNA-seq data
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