Error while trying out the TF Activity inference analysis section from the tutorial

[aditisk]

Hi again @enblacar,

I am getting an error while trying to get prior network information while following the TF activity inference vignette. The error is pasted below:

> network <- decoupleR::get_dorothea(organism = "human",levels = c("A", "B", "C")) Error: 'import_dorothea_interactions' is not an exported object from 'namespace:OmnipathR'

I am using SCpubr_1.0.1 and I manually downloaded all the required dependencies. Any thoughts on how to fix this ?

Thanks.

[enblacar]

Hi @aditisk,

Both SCpubr:: do_PathwayActivityPlot() and SCpubr:: do_TFActivityPlot() expect you to have run decoupleR beforehand.

For this, you will need to install it:

install.packages("BiocManager")
BiocManager::install("decoupleR")

However, since this is not required to plot the results, I have not put this package in the list of dependencies.

If it still does not work after installing decoupleR, please try installing OmnipathR as well. Also, please consider updating to SCpubr v1.0.2, as it has new features and bug fixes.

Closing this for now, if the error still persists let me know!
Enrique