haploR

haploR queries HaploReg and RegulomeDB from R to retrieve genome annotation and regulatory information for genetic variants to support post-GWAS interpretation.

Key Features:

• Integration with Genome Annotation Tools: haploR interfaces with HaploReg and RegulomeDB to retrieve annotations for specified variants from within R.
• Data Frame Output: Query results are compiled into structured data frames for downstream bioinformatic analyses.
• Facilitation of Post-GWAS Analysis: Provides annotation of regulatory elements and variant-level information to aid interpretation of GWAS-identified variants.

Scientific Applications:

• Post-GWAS variant annotation: Annotating GWAS-identified variants with regulatory information from HaploReg and RegulomeDB to prioritize candidate variants.
• Functional interpretation of regulatory variants: Supporting identification of regulatory elements and potential links to disease mechanisms or trait variation.

Methodology:

Leverages R's data manipulation capabilities to automate web queries to HaploReg and RegulomeDB and organizes returned annotations into data frames.