SCOTCH is a computational method that leverages the optimal transport algorithm and a cell matching strategy to integrate scRNA-seq and scATAC-seq data. SCOTCH takes into account the adverse effects of cell type abundance and cell number differences on data integration during the calculation process, and predicts cell pairing relationships to meet the needs of downstream in-depth analysis.

pip install scotch-sc

We have applied SCOTCH on different tissues of multiple species, here we give step-by-step tutorials for application scenarios. And datasets in .h5ad fomat can be downloaded from Google Drive.

• Using SCOTCH to integrate SHARE-seq data of mouse cerebral cortex

• Using SCOTCH to integrate human kidney snRNA-seq and snATAC-seq datasets

• Using SCOTCH to integrate mouse cerebral cortex MERFISH and scATAC-seq datasets

Should you have any questions, please feel free to contact the author of the manuscript, Mr. Penghui Yang ([email protected]).