Fig. 1

scDIOR workflow. a scDIOR contains two modules, where dior and diopy. scDIOR implements the single-cell data IO between R (Seurat, SingleCellExperiment and Monocle) and Python (Scanpy) through the hierarchical construction of HDF5 group, HDF5 dataset, and HDF5 attribute; b scDIOR create the ‘.h5’ file containing the groups of data, layers, obs, var, dimR, graphs, uns, and spatial. Column ‘Description’ is brief description of the group information. Column ‘R:Seurat object’, ‘R: SingleCellExperiment & Monocle3 object’, and ‘Python: anndata object (Scanpy)’ represents the groups corresponding to the slot of data in the Seurat, Singlecellexperiment(Monocle3), and anndata object. Column ‘R: data type’, ‘H5 data type’, and ‘Python: data type’ represents the common storage format of R and Python in ‘.h5’ file. The dgCMatrix means R Matrix package ‘dgCMatrix’ object. The matrix means R base package ‘matrix’ object. The data.frame means R base package ‘data.frame’ object. The list means R base package ‘list’ object. The csr_matrix means Python SciPy module ‘scipy.sparase.csr.csr_matrix’ object. The ndarray means Python NumPy module ‘numpy.ndarray’ object. The DataFrame means Python Pandas module ‘pandas.core.frame.DataFrame’ object. The dict means Python ‘dict’ object