GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis

Incomplete gene models negatively impact single-cell gene expression quantification. This is particularly true in non-model species where often gene 3' ends are inaccurately annotated, while most scRNA-seq methods only capture the 3' transcript region. This results in many genes being incorrectly quantified or not detected. GeneExt leverages scRNA-seq data to refine gene annotations, enhancing biological interpretation and cross-species comparisons of cell type expression atlases.