scPerturb Single-Cell Perturbation Data: RNA and protein h5ad files

This repository contains the single-cell RNA and protein datasets as h5ad files scRNA-seq and protein datasets within the scperturb database as h5ad files (saved with scanpy v1.9.1.) from the scperturb database.<br>In order to facilitate development and benchmarking of computational methods in systems biology, we collected a set of 44 publicly available single-cell perturbation-response datasets with molecular readouts, including transcriptomics, proteomics and epigenomics. We applied uniform quality control pipelines and harmonize feature annotations. The resulting information resource enables efficient development and testing of computational analysis methods, and facilitates direct comparison and integration across datasets. In addition, we describe E-statistics for perturbation effect quantification and significance testing, and demonstrate E-distance as a general distance measure for single-cell data as both a python (scperturb on PyPI) and R (scperturbR on CRAN) package.<br>See the associated publication for info on how the data was handled. We also have an interactive table (Data Explorer) on our website with metadata per dataset.