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.

本仓库包含scperturb数据库（scperturb database）中的单细胞RNA测序（scRNA-seq）与蛋白质组数据集，所有数据集均以h5ad格式存储，采用scanpy v1.9.1版本保存。为助力系统生物学领域计算方法的开发与基准测试，我们收集了44套公开可用的单细胞扰动响应数据集，均包含分子检测读数，涵盖转录组学、蛋白质组学与表观基因组学范畴。我们采用统一的质量控制流程对数据进行处理，并对特征注释进行了标准化整合。本数据集资源可支持计算分析方法的高效开发与测试，同时便于不同数据集间的直接比较与整合。此外，我们提出了用于扰动效应量化与显著性检验的E统计量（E-statistics），并验证了E距离（E-distance）作为单细胞数据通用距离度量的适用性；相关实现已分别封装为Python包（scperturb，可在PyPI获取）与R包（scperturbR，可在CRAN获取）。有关数据处理的详细细节，请参阅相关学术论文。我们的官方网站还提供了交互式数据表（数据探索器，Data Explorer），包含各数据集的元数据信息。