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 !

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