1 Introduction

This user manual provides a practical guide to using the RNAshapeQC package for RNA coverage-shape-based quality control metrics. It is designed for researchers who want to quantify RNA integrity, detect degraded or suboptimal samples, and visualize gene body coverage patterns across diverse RNA-seq datasets.

The manual covers:

  • preparing input files and directory structures
  • running the core QC functions
  • interpreting nonuniformity and coverage-shape metrics
  • generating reproducible figures and summary tables

Examples throughout the manual are based on subsets of real datasets (TCGA Pilot, TCGA-LUAD, and Alliance/CALGB) to illustrate workflows and outputs.