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ensemblQueryR: fast, flexible and high-throughput querying of Ensembl LD API endpoints in R

Fairbrother-Browne, Aine; García-Ruiz, Sonia; Hertfelder Reynolds, Regina; Ryten, Mina; Hodgkinson, Alan; (2023) ensemblQueryR: fast, flexible and high-throughput querying of Ensembl LD API endpoints in R. GigaByte , 2023 pp. 1-10. 10.46471/gigabyte.91. Green open access

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Abstract

We present ensemblQueryR, an R package for querying Ensembl linkage disequilibrium (LD) endpoints. This package is flexible, fast and user-friendly, and optimised for high-throughput querying. ensemblQueryR uses functions that are intuitive and amenable to custom code integration, familiar R object types as inputs and outputs as well as providing parallelisation functionality. For each Ensembl LD endpoint, ensemblQueryR provides two functions, permitting both single- and multi-query modes of operation. The multi-query functions are optimised for large query sizes and provide optional parallelisation to leverage available computational resources and minimise processing time. We demonstrate improved computational performance of ensemblQueryR over an exisiting tool in terms of random access memory (RAM) usage and speed, delivering a 10-fold speed increase whilst using a third of the RAM. Finally, ensemblQueryR is near-agnostic to operating system and computational architecture through Docker and singularity images, making this tool widely accessible to the scientific community.

Type: Article
Title: ensemblQueryR: fast, flexible and high-throughput querying of Ensembl LD API endpoints in R
Location: China
Open access status: An open access version is available from UCL Discovery
DOI: 10.46471/gigabyte.91
Publisher version: https://doi.org/10.46471/gigabyte.91
Language: English
Additional information: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Software and Workflows; Bioinformatics; Genetics; Software Engineering
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health > Genetics and Genomic Medicine Dept
URI: https://discovery.ucl.ac.uk/id/eprint/10177828
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