RDiff

RDiff: Differential RNA Processing Detection from RNA-Seq Data

RDiff detects differential RNA processing events from RNA-Seq data by identifying changes in isoform abundance and transcriptional activity across samples, with or without complete isoform annotations.

Key Features:

• rdiff.parametric: Parametric statistical test for well-annotated organisms that detects changes in relative isoform abundance using known isoform annotations.
• rdiff.nonparametric: Nonparametric test that detects differential read coverages, enabling analysis when isoform annotations are incomplete or absent.
• Count-Based Statistical Modeling: Models discrete RNA-Seq read counts and biological variability to produce statistically calibrated significance estimates.

Scientific Applications:

• Isoform Analysis: Identifies novel isoforms and quantifies known isoforms to characterize transcriptome dynamics.
• Differential RNA Processing: Detects changes in transcriptional and RNA-processing activity across experimental conditions.
• Cross-Species RNA-Seq Studies: Validated on RNA-Seq libraries from Arabidopsis thaliana and Drosophila melanogaster, with results consistent with RT-qPCR measurements.

Methodology:

RDiff applies parametric and nonparametric statistical tests to RNA-Seq read count data to evaluate differential isoform usage and read coverage patterns. Both approaches account for discrete count distributions and biological variability to generate calibrated significance estimates for differential RNA processing events.