Benchmarking atlas-level data integration in single-cell genomics - integration task datasets

Pancreas, Lung atlas, human immune cell, and human and mouse immune cell integration RNA integration tasks, and all ATAC mouse brain integration tasks from the manuscript "Benchmarking atlas-level data integration in single-cell genomics".

These datasets were aggregated from public datasets, cell annotations were harmonized or reannotated, and the data was consistently preprocessed using scran pooling and log+1 transformation (for RNA tasks). In the immune cell datasets an erythrocyte development trajectory was also annotated. Details on dataset preprocessing can be found in the paper and in the accompanying Github at https://www.github.com/theislab/scib.

Please cite the paper and the papers the individual datasets were aggregated from when using this data.