Critical evaluation of damaged cell quality control in single-cell RNA sequencing [Liver Case Study: Integrated filtered output]

Mouse liver dataset (GSE221481) containing four samples, underwent filtering by a damaged cell detection strategy before integration and cell type annotation. Sixteen filtering strategies were implemented, with the integrated output available in the following .rds files. These include eight tool-based strategies: DamageDetective, ddqc, DropletQC, miQC, SampleQC, scater (filter and PCA), and valiDrops. As well as eight manual strategies, including fixed thresholds (fixed_mito_5, fixed_mito_10, fixed_mito_25) and adaptive thresholds set using MAD (3+) outlier detection (mito, mito_ribo, mito_features, malat1, malat1_features).