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scDIOR Bridges Platforms of R and Python for Single-cell Data Transformation


Principle Investigator CHEN Jiekai’s group of Guangzhou Institutes of Biomedicine and Health (GIBH) of the Chinese Academy of Sciences has developed a software scDIOR for the single-cell data transformation between platforms of R and Python based on Hierarchical Data Format Version 5 (HDF5). The article was published in BMC Bioinformatics on January 6, 2022. 

Single-cell RNA sequencing is becoming highly effective at identifying cell states, reconstructing cell developmental trajectories, and unrolling cell spatial expressions. Various computational toolkits and platforms have been provided for single-cell data analysis. Those programmed in two languages- R and Python are widely used by researchers. 

However, the difference of data structure between platforms of R and Python caused the data sharing and conversion problem, especially for three popular toolkits: Scanpy, Seurat, and SingleCellExperiemnt. Currently, there is no efficient and user-friendly software for the data transformation of single-cell omics between platforms. Consequently, users spend much time on data Input and Output (IO) instead of conducting productive analysis. 

The team has created scDIOR, as a data IO ecosystem between three R toolkits (Seurat, SingleCellExperiment, Monocle) and a Python toolkit (Scanpy). Importantly, it accommodates a variety of data types across programming languages and platforms in an ultrafast way, including single-cell RNA-seq and spatial resolved transcriptomics data. With scDIOR, single-cell data can be transformed under the command of only a few codes in Integrated Development Environment or command line interface. It connects the analytical tasks of different platforms, making it easy to compare the performance of algorithms between them. 

scDIOR contains two modules, dior in R and diopy in Python. It is a versatile and user-friendly tool that implements single-cell data alteration between R and Python rapidly and stably. The software has been optimized according to the suggestions from test users. It is freely accessible at https://github.com/JiekaiLab/scDIOR. Feedback is welcome and could be emailed to the address feng_huijian@grmh-gdl.cn. 

scDIOR Bridges Platforms of R and Python for Single-cell Data Transformation