Single-cell Analysis / R package
SingleCellExperiment
Store expression matrices, gene and cell metadata, and embedding coordinates together in a standard R object.
Best fit
Analysts moving data between Bioconductor packages while keeping metadata aligned with cells and genes.
What you need
R and Bioconductor, with assay and metadata dimensions that match.
What to check
It provides a data structure. Other tools are needed for tasks such as normalization, clustering, or interactive exploration.