Comments (5)
Dear Steven,
- We frequently combine Dorothea regulons with Viper using the Dorothea R package. You can check the website here:
https://saezlab.github.io/dorothea
In the articles section, you can find two notebooks explaining how to run Dorothea regulons coupled with Viper on bulk and single cell data to obtain TF activity.
- Dorothea regulons are also available via OmnipathR (excepting the interactions with the lowest condifence level). You can check OmnipathR website:
https://saezlab.github.io/OmnipathR/
and in particular the vignette in the articles section and the function to import the regulons:
https://saezlab.github.io/OmnipathR/reference/import_dorothea_interactions.html
I hope this helps. Please, do not hesitate to come back with furter questions.
Best,
Alberto.
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Dear Steven,
The Dorothea package has an internal function to convert the TF-target interactions into regulon objects:
https://github.com/saezlab/dorothea/blob/master/R/helpers.R
Let me know if this is what you need.
Best regards,
Alberto.
from omnipathr.
from omnipathr.
Yeah. In principle they should work, the regulon object should be the same for both functions: viper and msViper
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