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saezlab / cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
https://saezlab.github.io/cosmosR/
GNU General Public License v3.0
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Problem with knitr package #28

Closed SwagatikaSahoo2023 closed 1 year ago

SwagatikaSahoo2023 commented 1 year ago

Dear COSMOSR Authors, I am currently running the tutorial.Rmd in R Studio. I am getting the below error while running the chunk for preparing the inputs.

"Error in preprocess_COSMOS_metabolism_to_signaling(meta_network = toy_network, : could not find function "preprocess_COSMOS_metabolism_to_signaling"

Please advise further. Best Swagatika Sahoo

adugourd commented 1 year ago

Hi,

thanks for your interest in running our tool :)

It's difficult to be sure what's going on with this limitted information, but it appears that the cosmos library is not loaded properlly if you get this error.

If you want a more detailled tutorial, you can also have a look here: https://github.com/saezlab/NCI60_cosmos

Cheers,

Aurelien

SwagatikaSahoo2023 commented 1 year ago

Dear Aurelien Thanks for your prompt reply. I installed the codes from the github page, as mentioned in the tutorial https://embl-ebi.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=318f7091-b6bf-44ee-939f-adb10121fc1b

Furthermore, I have also downloaded codes from NCI60_cosmos & saezlab/decoupleR github pages. I am following the steps as mentioned in the tutorial, and it continues to complain as,

"Error in preprocess_COSMOS_metabolism_to_signaling(meta_network = toy_network, : could not find function "preprocess_COSMOS_metabolism_to_signaling""

Please let me know if I am missing something.

P.S. I am running from tutorial.Rmd in the vignettes folder. Best Swagatika Sahoo

On Mon, May 8, 2023 at 5:13 PM Aurelien Dugourd @.***> wrote:

Hi,

thanks for your interest in running our tool :)

It's difficult to be sure what's going on with this limitted information, but it appears that the cosmos library is not loaded properlly if you get this error.

If you want a more detailled tutorial, you can also have a look here: https://github.com/saezlab/NCI60_cosmos

Cheers,

Aurelien

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gabora commented 1 year ago

When you call library(cosmosR) do you get any error?