scPerturb Single-Cell Perturbation Data: ATAC files

This repository contains the scATAC-seq datasets from the scperturb database. For each dataset this includes the following feature matrices:ChromVarLSI_embeddinggene_scoresmarkerpeak_targetpeak_bcIn 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.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.