RNAshapeQC

RNA Coverage-Shape-Based Quality Control Metrics

Description

RNAshapeQC provides coverage-shape-based quality control (QC) metrics for mRNA-seq and total RNA-seq data. It supports per-gene pileup construction from BAM files as well as toy datasets for quick-start examples. The package implements protocol-specific metrics, including decay rate (DR), degradation score (DS), mean coverage depth (MCD), window coefficient of variation (wCV), area under the curve (AUC), and shape-based sample-level indices.

RNAshapeQC also includes HPC-friendly functions for per-gene batch processing and cross-study pileup generation. This package enables interpretable, protocol-specific QC assessments for diverse RNA-seq workflows.

Documentation

Comprehensive documentation is available in the Tutorial and the User Manual.

Installation

From GitHub

if (!requireNamespace("devtools", quietly=TRUE)) {
  install.packages("devtools")
}
devtools::install_github("hyochoi/RNAshapeQC", dependencies=TRUE)

From Bioconductor

if (!requireNamespace("BiocManager", quietly=TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install("RNAshapeQC", dependencies=TRUE)

Citation

If you use RNAshapeQC in your research, please cite the package using:

citation("RNAshapeQC")

A manuscript describing the methodology and applications of RNAshapeQC is currently in preparation. Citation information will be updated upon publication.