QClus: a droplet filtering algorithm for enhanced snRNA-seq data quality in challenging samples.

ABSTRACT: Single-nuclei RNA sequencing remains a challenge for many human tissues, as incomplete removal of background signal masks cell-type-specific signals and interferes with downstream analyses. Here, we present Quality Clustering (QClus), a droplet filtering algorithm targeted toward challenging samples. QClus uses additional metrics, such as cell-type-specific marker gene expression, to cluster nuclei and filter empty and highly contaminated droplets, providing reliable filtering of samples with varying number of nuclei and contamination levels. In a benchmarking analysis against seven alternative methods across six datasets, consisting of 252 samples and over 1.9 million nuclei, QClus achieved the highest quality in the greatest number of samples over all evaluated quality metrics and record

SUBMITTER: Schmauch E 

PROVIDER: S-EPMC11724311 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature