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Frequently Asked Questions

Compiled: February 28, 2024

Source: vignettes/articles/FAQ.Rmd

Can I cite scCustomize?

Yes! If you use scCustomize in your research I would really appreciate citing the package. The package can be cited as:

Marsh SE (2021). scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing. https://doi.org/10.5281/zenodo.5706430. RRID:SCR_024675.

Only journals in Cell Press family require the RRID # but great to include as part of reference citation and in methods section regardless of journal.

Something isn’t working

If you run into any issues or bugs please submit a GitHub Issue with details of the issue.

  • Please include the code that you are running and the full text of the error message.
  • If possible please include a reproducible example. Suggest using SeuratData package pbmc3k dataset for lightweight example.

Please note though scCustomize is currently one-person operation and I may not respond right away. I’m going to aim to respond to all issues posted during the week by Friday of that week so please be patient and know that I will work to solve your issue.

New Features/Enhancements

New features and enhancing current functions are always in my mind but again my bandwidth on other projects will dictate how quickly I can implement new features/enhancements.

If you have idea and code to implement new feature/enhancement Pull Requests are welcome for bug fixes, new features, or enhancements.

  • Please set PR to merge with “develop” branch and provide description of what the PR contains (referencing existing issue(s) if appropriate).

I have idea for new feature/enhancement but don’t know how to accomplish/write code for it.
That’s totally fine! Post your idea as a GitHub Issue and I will get back to you.

Does scCustomize support formats other than Seurat Objects?

Yes, though not extensively. Currently the package is primarily centered around interactivity with Seurat Objects with some functionality with LIGER objects (see LIGER Vignette) as well as some functions which can interact with raw data, base R data.frames, tibbles, and ggplot2 objects.

  • If users are interested in adapting functions (or creating separate functions) to provide comparable functionality with SCE or other object formats I would be happy to add them. See above for more info on PRs.

Installation Issues

Please see Installation page for more detailed installation instructions. If the issue persists please submit GitHub issue.