keyes-timothy / tidytof Goto Github PK

Hi Timothy,

I have been exploring this package's functionality after searching for tidy flow cytometry packages. I wanted to thank you for your efforts in this area and raise some ideas/questions based on my particular use case below.

I am leveraging automated methods of QC/QA, compensation, gating, and data visualization and analysis for flow cytometry. After doing a standard preprocessing pipeline for the compensation, QC, and then saving output fcs files (using common set of packages like flowCore, PeacoQC, opencyto, etc.), I am loading the QC'd FCS files into your framework, which is working well.

I see a lot of benefit at this stage of the analysis to moving into a tidy framework such as ability to wrangle the data (set a threshold gate using unstained samples), ability to cluster, visualize by specific event, model, do stats, etc. while incorporating sample/experimental metadata.

I'm wondering if you are planning for this package to support some of the above analytical steps I mention (compensation, QC, etc.) and also gating (e.g., load a gatingset from opencyto R package, loading FlowJo gating output, or direct manual/automated gating on the tidy data). I think much of this functionality is provided by other packages (requiring a different data format such as flow set). It would be useful if these could be directly incorporated into the tidy workflows you are developing. This could facilitate important analysis such as comparing gates with the dimensionality reduction outputs and other useful functionality your package provides.

I would be happy to discuss above request with you if interested.

Kind regards,

Gabe

We were asked by reviewers to provide changelogs for each package. Pkgdown will render these nicely if you add a NEWS.md file. You don't have to back-date, you can just start now and keep track of changes going forward.

https://nullranges.github.io/nullranges/news/index.html

https://github.com/nullranges/nullranges/blob/HEAD/NEWS.md