GTEx_Pro: A robust and accurate preprocessing pipeline for GTEx data: TMM+CPM normalization and SVA batch correction for enhanced multi-tissue analysis

Abstract

GTEx_Pro is a Nextflow-based pipeline for preprocessing GTEx v8 transcriptomic data, enhancing multi-tissue comparability. It integrates TMM + CPM normalization and SVA batch effect correction to improve biological signal recovery while reducing systematic variations across 54 GTEx tissues. Designed for scalability and reproducibility, GTEx_Pro facilitates accurate multi-tissue transcriptomic analysis and a similar framework can be adapted to other large-scale transcriptome datasets.