Reviewer name and names of any other individual's who aided in reviewer	Aziz Khan
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?	No
Additional Comments	There are two license files (the LICENSE, LICENSE.md) and both are conflicting. The authors should use one to make sure it is an appropriate Open Source Initiative license.
As Open Source Software are there guidelines on how to contribute, report issues or seek support on the code?	No
Additional Comments	There are no guidelines on how to contribute.
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	Installation was straightforward.
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	The DESCRIPTION file has all the required packages.
Have any claims of performance been sufficiently tested and compared to other commonly-used packages?	No
Additional Comments
Additional Comments
Are there (ideally real world) examples demonstrating use of the software?	Yes
Additional Comments	There are some use cases in the minimal documentation. Some of these are not working.
Is automated testing used or are there manual steps described so that the functionality of the software can be verified?	Yes
Additional Comments	The package is already in the CRAN, which means it passed its checks. It does have example snippets of code to be run.
Any Additional Overall Comments to the Author	The ensemblQueryR package offers an R interface for querying Ensembl REST API linkage disequilibrium (LD) endpoints. The package aims to support high-throughput querying, utilizing familiar R object types and parallelization. The package is already in CRAN and comes with Docker/Singularity options. While the paper highlights notable strengths, such as the R interface, high-throughput support, parallelization, and performance improvements, a few points warrant further consideration and clarification. (1). The package is already in CRAN, which is good, but there are issues with the use-case examples. When I executed the test case to query LD metrics for a variant within a window, the package returned a tibble containing NAs. (2). The title claims the package supports querying "several" Ensembl API endpoints, but the current version is limited to LD endpoints. Revising the title to reflect the package's current capabilities accurately is recommended. (3). Two conflicting license files exist (the LICENSE, LICENSE.md). The authors should select one to ensure it aligns with an appropriate Open Source Initiative license. Additionally, there are no guidelines provided for contributing to the project. (4). I have encountered this R package to get Ensembl data in R using the REST API - https://github.com/dwinter/rensembl. Can the authors comment on this?
Recommendation	Minor Revisions