Error runing runBBKNN function & Shiny app not working

[siwending]

I encountered a problem when I correct the batch effect with the runBBKNN method. Here is the code I used:
sce <- scaterlogNormCounts(inSCE = sce, useAssay = 'counts', assayName = 'logcounts')
sce <- runBBKNN(inSCE = sce, batch="orig.ident")
And here is what I got:

However, I'm pretty sure bbknn was installed, but R failed to recognize it. When installing singlecellTK, I followed the guide, and ran the followling command, but bbknn was still not recognized by R.

Also, the shiny app does not seem to be working at this moment.

Any help will be greatly appreciated! Thank you!

Best,
Bella

[joshua-d-campbell]

Hi @siwending, thanks for trying out our tool. It is a bit hard to diagnose from this information. Could you run the following code:

reticulate::py_config()

This will tell us what version of python is being used. It is possible that another version of python is currently being selected. Once a version is selected, it can't be unselected until R is restarted. Also could you run:

sessionInfo()

So we can see the versions of the packages you are currently using.

Lastly, we have restarted the online app, so it should be working now.

[siwending]

Hi @joshua-d-campbell, thanks for getting back to me! Here is the result from reticulate::py_config():

From py_config, it shows that the version of python being used comes from the sctk-reticulate condo env install from the sctkPythonInstallConda() command. It should be correct.

And here is what I get from sessionInfo():

I follow the singleCellTK installation tutorial to install the package, but it seems like the version is 2.10.0 which higher than the released 2.8.1. Not sure what is going on here. Will this cause the entire issue?

Again, appreciate all of your effort!

Thanks,
Bella