traseR

traseR performs enrichment analysis of trait-associated single nucleotide polymorphisms (SNPs) within user-defined genomic intervals to connect GWAS-identified variants to phenotypic traits and potential regulatory mechanisms.

Key Features:

• Enrichment Analysis: Identifies enrichment of trait-associated SNPs within specified genomic intervals.
• Trait-associated SNP Catalog: Integrates a comprehensive catalog of trait-associated SNPs for analysis.
• Flexible Statistical Testing: Provides multiple hypothesis-testing approaches for enrichment assessment.
• Background Options: Supports different background definitions for enrichment testing to account for genomic context.
• Linkage Disequilibrium (LD) Consideration: Includes functionality to account for SNPs in linkage disequilibrium.
• Visualization and Exploration: Produces visualizations to explore and interpret enrichment results.

Scientific Applications:

• GWAS Interpretation: Linking GWAS-identified variants to genomic regions to prioritize candidate loci.
• Regulatory Mechanism Inference: Inferring potential regulatory mechanisms and pathways implicated by enriched SNPs.
• Translational Discovery: Supporting translational studies to identify candidate therapeutic targets from enriched variant loci.

Methodology:

Integrates a catalog of trait-associated SNPs with user-defined genomic intervals, applies flexible statistical hypothesis tests for enrichment, allows alternative background definitions, and accounts for linkage disequilibrium.