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saezlab / OmnipathR

R client for the OmniPath web service
https://r.omnipathdb.org/
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R script for viper with OmnipathR regulons #17

Closed StevenVanLaere closed 4 years ago

StevenVanLaere commented 4 years ago

Dear Julio,

Do you have a script on how to combine regulon data from OmniPathR with the BioConductor package “viper”?

Much appreciated. Thanks.

Steven Van Laere

alberto-valdeolivas commented 4 years ago

Dear Steven,

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.

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.

StevenVanLaere commented 4 years ago

Dear Alberto,

Thanks for your answer.

I was going through the vignette of the viper package, and I got particularly interested in the synergy and shadow analysis that comes with the msViper function. I can see that the run_viper function from the dorothea package uses regulons in table format, and I wonder if this is possible for the msViper function too. At the moment I can only see that the latter runs with a proper regulon object. Is there a way to generate the regulon objects?

Thanks.

Steven

Op 15 jun. 2020, om 20:24 heeft Alberto Valdeolivas notifications@github.com het volgende geschreven:

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 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/ 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 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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alberto-valdeolivas commented 4 years ago

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.

StevenVanLaere commented 4 years ago

Dear Alberto,

Thanks! I will give it a shot. The resulting regulons also work with msViper?

Thanks a lot.

Steven

Op 18 jun. 2020, om 09:13 heeft Alberto Valdeolivas notifications@github.com het volgende geschreven:

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 https://github.com/saezlab/dorothea/blob/master/R/helpers.R Let me know if this is what you need.

Best regards, Alberto.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/saezlab/OmnipathR/issues/17#issuecomment-645827101, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB7ZTVJFTFMHRAQ5F3IPT7LRXG5CNANCNFSM4N6K5Y6A.

alberto-valdeolivas commented 4 years ago

Yeah. In principle they should work, the regulon object should be the same for both functions: viper and msViper