CellCov: gene-body coverage profiling for single-cell RNA-seq

Abstract

MotivationGene-body coverage bias differs across scRNA-seq protocols and can influence downstream analyses, yet coverage is often assessed using bulk-level summaries that obscure cell-to-cell variability. ResultsCellCov provides gene-body coverage profiling at single-cell resolution, enabling exploration of coverage heterogeneity across both cells and features. The accompanying workflow supports flexible grouping and robust aggregation of profiles by user-provided annotations, allowing principled comparison of coverage bias across sequencing protocols. We demonstrate its use on public datasets from several full-length scRNA-seq chemistries. AvailabilityCellCov source code and documentation are available at https://github.com/ziegenhain-lab/CellCov Contactchristoph.ziegenhain@ki.se Supplementary informationSupplementary data are available at Bioinformatics online