Data Analysis and Benchmarking
A test metric for assessing single-cell RNA-seq batch correction
Büttner et al. (Nature Methods, 2018)
kBET is a user-friendly, robust and sensitive k-nearest-neighbor test for the quantification of batch effects.
Benchmarking atlas-level data integration in single-cell genomics
Lücken et al. (Nature Methods, 2021)
We provide a benchmark of 68 combinations of single-cell integration and preprocessing methods applied to 85 technical batches of gene expression, chromatin accessibility and simulation data from 23 publications, altogether representing >1.2 million cells distributed in 13 atlas-level integration tasks.
An integrated cell atlas of the human lung in health and disease
Sikkema et al. (biorXiv, 2022)
The integrated Human Lung Cell Atlas (HLCA) combines 46 datasets of the human respiratory system into a single atlas spanning 2.2 million cells from 444 individuals across health and disease.