Ularcirc

Ularcirc analyzes circular RNAs by integrating backsplice junction (BSJ) and canonical forward splicing data to characterize circRNA biogenesis and expression across samples.

Key Features:

• Integration of Splicing Data: Combines analysis of backsplice junctions (BSJs) and canonical forward splicing junctions to relate circRNA junctions to parental transcript splicing.
• Data Compatibility: Accepts and assembles BSJ information from STAR aligner outputs and circRNA callers CIRI and circExplorer.
• Multi-Sample BSJ Quantification: Constructs BSJ count tables enabling comparison of circRNA expression across multiple samples.
• Visualization of Splicing Junctions: Generates visualizations of BSJs and canonical splicing junctions to support interpretation of circRNA structure.
• Downstream circRNA Analyses: Supports downstream analyses for discovery of novel splicing patterns and characterization of circRNAs, including identification of candidates with potential open reading frames longer than their linear counterparts.
• Detection of Internal Splicing Events: Detects internal splicing events within circRNAs to reveal structural complexity.
• BSJ Formation Complexity Analysis: Facilitates analysis of the complexity of BSJ formation and splicing relationships in parental transcripts.
• Gene Annotation: Annotates circRNAs with overlapping gene information using Bioconductor resources.

Scientific Applications:

• Discovery of Novel Splicing Patterns: Enables identification of novel splicing events in parental transcripts associated with circRNA formation.
• Detection of Internal Splicing Events: Facilitates identification of internal splicing within circRNAs to map exon composition.
• Analysis of BSJ Formation Complexity: Enables study of mechanisms and complexity underlying BSJ formation.
• Identification of Novel circRNA Classes: Supports detection and validation of novel circRNA classes, for example circRNAs derived from ApoA4 transcripts with non-canonical splicing sites within coding exons.

Methodology:

Assembles BSJ count tables from outputs of the STAR aligner, CIRI, or circExplorer to support multi-sample analysis and downstream analyses, and annotates circRNAs with overlapping gene information from Bioconductor databases.