RNAshapeQC

RNAshapeQC provides coverage-shape-based quality control metrics for mRNA-seq and total RNA-seq data to enable interpretable, protocol-specific QC assessments.

Key Features:

• Per-gene pileup construction: Constructs per-gene pileups from BAM files.
• Toy datasets: Includes toy datasets for quick-start examples.
• Protocol-specific metrics: Implements 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.
• HPC-friendly batch processing: Provides functions for per-gene batch processing and cross-study pileup generation.

Scientific Applications:

• RNA-seq quality control: Enables interpretable, protocol-specific QC assessments for diverse mRNA-seq and total RNA-seq workflows.

Methodology:

RNAshapeQC computes coverage-shape-based metrics from per-gene pileups constructed from BAM files.