PerturbSeq.db: An Integrated Repository for Comprehensive Analysis of Single-cell Perturbation Data

Single-cell perturbation studies have emerged as a transformative approach in biological research, offering unprecedented insights into cellular responses to genetic and chemical interventions. However, the field faces challenges related to data accessibility and integration. To address this, we present PerturbSeq.db (http://bioailab.com/PerturbSeq.db/), a comprehensive database that consolidates and harmonizes single-cell perturbation datasets from a diverse array of sources. PerturbSeq.db comprises 189 datasets from 77 studies, including 165 scRNA-seq and 24 scATAC-seq datasets, spanning approximately 50 distinct cell lines or tissues. To ensure data consistency and comparability, PerturbSeq.db employs a uniform processing pipeline across all datasets. The database is complemented by an interactive, user-friendly interface that facilitates efficient data exploration and analysis, empowering researchers to navigate the complexities of single-cell perturbation data. Overall, PerturbSeq.db serves as a critical resource for the scientific community, providing a comprehensive, well-annotated collection of datasets for analyzing and interpreting the effects of perturbation at the single-cell level.