Reviewer name and names of any other individual's who aided in reviewer	Joost Wagenaar
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	There is a clear statement of need, but the audience is not very targeted. The investigators outline the need for tools to help users identify phenotypic subtypes of disease and describe how the tool would help with this. Although the investigators mention that the tool will allow users to analyze biomarker data, the scope of the types of analysis that can be performed is relatively small. I think that it would benefit the tool to better define the targeted users (clinicians, data scientists, enthusiasts?) and develop specifically towards a single audience. The tool leverages several existing R packages to run the analysis over the data and the provided tool can be described as a user-friendly wrapper around these libraries. The interface allows users to submit a file, and plot the results of the analysis within the app.
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?	No
Additional Comments	I did not see any guidelines for contributing to the project in the paper, or in the associated GitHub repository.
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	Yes, the investigators did a great job providing documentation and installation instructions.
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	Yes, the investigators provide a clearly-stated list of dependencies and instructions on how to install them prior to running the application.
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)?	Yes
Additional Comments	The paper, and GitHub repository point to a public dataset that can be used to test the application.
Are there (ideally real world) examples demonstrating use of the software?	Yes
Additional Comments	The investigators provide a video highlighting the use of the application and provide a use-case where they use the app to validate some existing knowledge.
Is automated testing used or are there manual steps described so that the functionality of the software can be verified?	No
Additional Comments	The application is sufficiently small that no automated testing or manual testing would necessary be required beyond validating that the application works.
Any Additional Overall Comments to the Author	The proposed application provides a nice tool that makes visualization of vcf data and analysis easier for users who are not comfortable working within R directly. It provides a nice demonstration how the scientific community can wrap scientific tools into deployable applications and tools that can be easily understood. A question remains on the target audience for an application like this as most people who are interested in these type of analysis and visualizations are, in fact, familiar enough with R, or other programming languages to directly leverage the libraries and plot the results. That said, as data integration and multi-omics visualization becomes more complex and the app provides more ways to visualize the data in meaningful ways, I do strongly believe that applications like this can provide a meaningful addition to the scientific tools that are available.
Recommendation	Accept