Review of scSTEM repo

[marouenbg]

Overall, it is very easy to install scSTEM using the first option and run it, it is very accessible.
I have a few minor comments:

• it would be nice to abstract a few steps by the command line, for example: the download of lock file could be done through a command like curl -O file.lock
• Also, you can specify the example path only once in the beginning as a variable for example path <- 'home/alex/sctem' and then refer to that variable for the remainder of the tutorial.
• You can also include the installation of the trajectory inference software as a dependency
• Finally, it would be nice to have an example button in the GUI that preloads some toy example data or even real world data.

Fantastic tool overall!

[alexQiSong]

Thanks for the comments, very helpful!

[marouenbg]

For the second round, I suggest the following:

• add releases to STEM, you can use GitHub release to add a microversion everytime you push new code/bug fix. For example, when the new GUI, this can be SCSTEM 0.1.1
• In README
  install_folder = "/home/alex/scstem/"
  renv::restore(project = install_folder, lockfile = paste0(install_folder,"renv.lock"), prompt = F)
• In README
  add a section on how to update scTEM if a new release is developed. That would be through
  1- devtools::install_github("alexQiSong/scSTEM", upgrade = "always") then 2-restart Rstudio.
• In GUI, the infer trajectory button could use a more expressive icon than a folder, I am not sure how shiny works, but if this is possible you can use icons from https://fontawesome.com/

Great job developing this phenomenal tool @alexQiSong !

[alexQiSong]

Thanks for the comments! Sorry to get back to this a bit late. Thank you, Alex ------ (Alex) Qi Song, Ph.D. Postdoctoral Associate Computational Biology Department School of Computer Science Carnegie Mellon University Pittsburgh, PA 15213

…

On Mon, Nov 1, 2021 at 8:45 PM Marouen ***@***.***> wrote: For the second round, I suggest the following: - add releases to STEM, you can use GitHub release to add a microversion everytime you push new code/bug fix. For example, when the new GUI, this can be SCSTEM 0.1.1 - In README install_folder = "/home/alex/scstem/" renv::restore(project = install_folder, lockfile = paste0(install_folder,"renv.lock"), prompt = F) - In README add a section on how to update scTEM if a new release is developed. That would be through 1- devtools::install_github("alexQiSong/scSTEM", upgrade = "always") then 2-restart Rstudio. - In GUI, the infer trajectory button could use a more expressive icon than a folder, I am not sure how shiny works, but if this is possible you can use icons from https://fontawesome.com/ Great job developing this phenomenal tool @alexQiSong <https://github.com/alexQiSong> ! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGEEJ5FGKJAGYO3NENJHZV3UJ4YBNANCNFSM5FR4FGCA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.