SCANVIS

SCANVIS annotates and scores splice junctions (SJs) from RNA-seq to quantify and visualize tissue-specific splicing signatures for association with disease.

Key Features:

• Annotation-dependent scoring: Scores and annotates splice junctions using annotation details from GENCODE and other genomic databases.
• Relative Read Support scoring: Implements the Relative Read Support scoring method to preserve tissue specificity of splicing signatures.
• Sashimi plot integration: Incorporates annotation details into sashimi plots for RNA-seq visualization of complex splicing events.
• Visualization of frame-shifts and annotation support: Produces visualizations that highlight frame-shifts and annotation support at both individual-sample and cohort levels.
• Per-sample and cohort analysis: Supports analysis and comparison of splice junctions across individual samples and sample cohorts.

Scientific Applications:

• Disease association and biomarker discovery: Enables association of splicing signatures with disease for prognosis, diagnosis, and therapeutic development.
• Tissue-specific splicing analysis: Facilitates analysis of tissue-specific splicing patterns across samples and cohorts.

Methodology:

Uses annotation-dependent scoring (including GENCODE annotations) and the Relative Read Support scoring method, integrates annotations into sashimi plot visualizations, and demonstrates capabilities using publicly available RNA-seq samples.