ensemblQueryR

ensemblQueryR queries Ensembl linkage disequilibrium (LD) endpoints to retrieve LD data for high-throughput genetic analyses.

Key Features:

• R-based interface: Implements R functions that accept and return familiar R object types for direct integration with R-based analyses.
• High-throughput querying: Supports single-query and multi-query modes optimized for handling large LD query sets.
• Parallelisation: Offers optional parallelisation to distribute queries across available computational resources.
• Computational performance: Demonstrates approximately a 10-fold increase in speed and uses about one-third of the random access memory (RAM) compared to existing tools.
• Cross-platform distribution: Distributed with Docker and Singularity images to enable deployment across different operating systems and architectures.

Scientific Applications:

• Linkage disequilibrium analysis: Retrieval of LD metrics from Ensembl LD endpoints for analysis of genetic linkage patterns.
• Genome-wide association studies (GWAS): Large-scale LD data retrieval to support variant association interpretation and fine-mapping.
• Population genetics: Access to LD data for population-level analyses of genetic structure and haplotype relationships.

Methodology:

Implements R functions to query Ensembl LD endpoints in single-query and multi-query modes with optional parallelisation and is distributed via Docker and Singularity images.