Reviewer name and names of any other individual's who aided in reviewer	Andy Yates
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published manuscript. (If no, please inform the editor that you cannot review this manuscript.)	Yes
Is the language of sufficient quality?	Yes
Please add additional comments on language quality to clarify if needed
Is there a clear statement of need explaining what problems the software is designed to solve and who the target audience is?	Yes
Additional Comments
Is the source code available, and has an appropriate Open Source Initiative license <a href="https://opensource.org/licenses" target="_blank">(https://opensource.org/licenses)</a> been assigned to the code?	Yes
Additional Comments
As Open Source Software are there guidelines on how to contribute, report issues or seek support on the code?	Yes
Additional Comments	Whilst nothing explicit is there the code is hosted on GitHub & therefore using the issue tracker would appear to be the right way to do this
Is the code executable?	Yes
Additional Comments
Is installation/deployment sufficiently outlined in the paper and documentation, and does it proceed as outlined?	Yes
Additional Comments
Is the documentation provided clear and user friendly?	Yes
Additional Comments
Is there enough clear information in the documentation to install, run and test this tool, including information on where to seek help if required?	Yes
Additional Comments
Is there a clearly-stated list of dependencies, and is the core functionality of the software documented to a satisfactory level?	Yes
Additional Comments
Have any claims of performance been sufficiently tested and compared to other commonly-used packages?	Yes
Additional Comments
Is test data available, either included with the submission or openly available via cited third party sources (e.g. accession numbers, data DOIs)?	No
Additional Comments	The code uses data from Ensembl so this is somewhat sufficient and uses rsIDs
Are there (ideally real world) examples demonstrating use of the software?	Yes
Additional Comments
Is automated testing used or are there manual steps described so that the functionality of the software can be verified?	Yes
Additional Comments
Any Additional Overall Comments to the Author	The authors present in their manuscript “ensemblQueryR: fast, flexible and high-throughput querying of Ensembl API endpoints in R”; a library for the popular R programming language and specifically addresses fast retrieval of linkage disequilibrium from Ensembl’s REST APIs. The toolkit provides a convenient set of functions which mediates queries into the Ensembl REST API and presents results in a manner which is optimised and familiar for R users. Overall I find the manuscript good and provides a useful toolkit for R developers. It is pleasing to see more people use the Ensembl REST APIs and to expand its user base. The analysis benchmarks also appear appropriate. I have only two minor comments. 1. Code examples Whilst I was able to execute the given example I did encounter some issues. Namely that when executing the code ensemblQueryR::ensemblQueryLDwithSNPwindow(rsid="rs4129267", r2=0.8, d.prime=0.8, window.size=500, pop="1000GENOMES:phase_3:EUR") I got the following result query snp_in_ld r2 d_prime population_name <chr> <lgl> <lgl> <lgl> <lgl> 1 rs4129267 NA NA NA NA It was disconcerting to not get any results back and now I am unsure if I did the right thing. I then found the GitHub repository was a far better reference for the correct commands to run and would encourage perhaps less information in the manuscript and the authors pointing readers to the GitHub repository or the site https://ainefairbrother.github.io/ensemblQueryR/. 2. Extensions The authors suggest possible extensions to ensemblQueryR but it would be useful to know if there are any specific developments planned by the authors.
Recommendation	Minor Revisions