CARTEpigenoQC: A Quality Control Toolkit for CAR-T Single-Cell Epigenomic Data

Abstract: CARTEpigenoQC is an R-based toolkit designed to streamline quality control (QC) for single-cell epigenomic datasets involving Chimeric Antigen Receptor (CAR)-engineered T cells. With the growing application of scATAC-seq, scCUT&Tag, and scBS-seq to characterize CAR-T cell states, it has become critical to perform customized QC that not only addresses standard metrics like FRiP (Fraction of Reads in Peaks) and TSS enrichment, but also directly detects signal from CAR vector insertion sites. CARTEpigenoQC supports both 10x Genomics and non-10x data formats and produces HTML and PNG summary outputs suited for exploratory analysis and regulatory-grade preclinical reporting. It is intended to assist researchers, core facilities, and translational immunologists in ensuring the validity of single-cell epigenomic profiling of engineered T cells.