scDiagnostics: systematic assessment of cell type annotation in single-cell transcriptomics data

This dataset contains four processed single-cell expression objects used in the manuscript "scDiagnostics: diagnostic tools for assessing cell type annotation quality in single-cell RNA-seq data" (Christidis et al.). Included files: covid_data_sce.rds — COVID-19 PBMC query dataset (severe infection), annotated with SingleR, Azimuth, CellTypist, and scArches normal_data_sce.rds — Healthy control PBMC reference dataset dss9_data.rds — DSS-induced colitis MERFISH query dataset (day 9), annotated with SingleR, Azimuth, CellTypist, and scArches healthy_data.rds — Healthy mouse colon MERFISH reference dataset All objects are SingleCellExperiment (or SpatialExperiment for MERFISH) format with complete cell type annotations and metadata in colData(). Usage: Download these files and place in your local data/covid/ and data/merfish/ directories. See the scDiagnostics Manuscript Repository for full analysis code and tutorials. Citation: Please cite the manuscript and this dataset when using these objects in your work.