OmnipathR

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How to get information about downstream target genes of ligands and receptors in cell interactions?

2

Hi, Thank you very much for your Omnipath database. Now I have some information about ligands and receptors, but I want to know what are the transcription factors and target...

qijt123

Trying to run: ```R library(OmnipathR) library(nichenetr) nichenet_results

j-bac

I think that there is more evidence that point toward CDK6 being a classic inhbitor of RUNX1 than activation.

adugourd

It seems that a lot of scientist love to refer to PDPK1 as PDK1 in their papers (e.g. : “This molecule recruits protein kinase B (PKB, also called Akt) and...

adugourd

OmniPath failling to install in GH action

1

Hi, I'm using the `pkgdown` GitHub action, in my package I'm using OmniPathR, though it seems that it cannot be installed in the `r-lib/actions/setup-r-dependencies@v2` step of the GH action. Below...

joan-yanqiong

kegg_pathways_download returns fewer pathways

1

Hello, Thank you so much for creating this fantastic package! I used " kegg_pathways_download" to download all kegg pathways. I am confused it says "downloaded 551 records" but in the...

cchen22

Error when running "net <- get_collectri(organism='human', split_complexes=FALSE)"

1

Hi, I am trying to run the decoupleR pipeline for TF enrichment analysis. Please help. Trying the code using OmnipathR: > net sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-pc-linux-gnu (64-bit)...

kasayadior

Hi, I am implementing the Omnipath resources for NicheNet analysis on a Windows computer. I was optimizing the parameters for the model as shown below: ``` # Parameter optimization expression_settings_validation

tkapello