DuplexDiscovereR

DuplexDiscovereR analyzes data from RNA cross-linking and proximity ligation protocols to identify and characterize RNA-RNA interactions from chimerically or split-aligned reads.

Key Features:

• Alignment Processing: Accepts chimerically or split-aligned reads as input for downstream analysis.
• Alignment Classification and Filtering: Includes procedures for classification and filtering of aligned reads.
• Duplex Group Clustering: Efficiently clusters individual chimeric reads into duplex groups (DGs).
• RNA Duplex Prediction: Predicts RNA duplex formation and calculates their hybridization energies.
• Statistical Metrics: Calculates p-values for random ligation hypothesis and mean DG alignment scores to rank RNA duplexes.
• Replicate Comparison: Processes data from multiple experiments or replicates separately for reproducibility assessment.
• Computational Efficiency: Achieves superior or comparable prediction quality with significantly improved time and memory efficiency compared to existing methods.
• Interoperability: Results integrate seamlessly with commonly used bioinformatics tools for transcriptomics in R.
• Protocol Adaptability: Readily adaptable to analyzing data from different experimental protocols.

Scientific Applications:

• Transcriptome-wide RNA-RNA Interaction Mapping: Identifies cis and trans RNA-RNA interactions from duplex data generated by high-throughput sequencing.
• SPLASH Data Analysis: Processes data from the SPLASH protocol for RNA cross-linking and proximity ligation.
• PARIS Data Analysis: Processes data from the PARIS protocol for RNA cross-linking and proximity ligation.
• LIGR-seq Data Analysis: Processes data from the LIGR-seq protocol for RNA cross-linking and proximity ligation.
• Experimental Reproducibility Assessment: Compares data from multiple experiments or replicates to check reproducibility of the experimental method.

Methodology:

DuplexDiscovereR clusters individual chimeric reads into duplex groups (DGs), predicts RNA duplex formation and hybridization energies, and calculates p-values for random ligation hypothesis and mean DG alignment scores to rank RNA duplexes.