DropletUtils

DropletUtils provides algorithms and utilities for processing droplet-based single-cell RNA-seq (scRNA-seq) data, enabling statistical identification of cell-containing droplets from ambient RNA and correction of barcode swapping in multiplexed 10X Genomics/Illumina datasets.

Key Features:

• Cell identification from empty droplets: Identifies cell libraries by detecting significant deviations in expression profiles from the ambient solution to recover low UMI-count cells while controlling the false discovery rate.
• Barcode swapping correction: Detects and excludes individual molecules affected by barcode swapping on patterned flow cell Illumina sequencers by leveraging the combinatorial complexity of 10X Genomics experiments.
• Data handling utilities: Provides functions for loading datasets, removing barcode-swapped pseudo-cells, and downsampling the count matrix.

Scientific Applications:

• Quality control for droplet-based scRNA-seq: Improves cell calling and ambient RNA discrimination to retain genuine low-UMI cells and enhance downstream single-cell transcriptomic analyses.
• Multiplexed scRNA-seq experiments: Mitigates artefacts from barcode swapping in multiplexed 10X Genomics studies sequenced on Illumina patterned flow cells to preserve sample integrity.

Methodology:

Uses a statistical cell-calling method that detects deviations from ambient expression profiles and controls false discovery rate; applies an algorithm that identifies and excludes molecules affected by barcode swapping by exploiting combinatorial barcode complexity; includes functions to load data, remove barcode-swapped pseudo-cells, and downsample count matrices.