Dynamic PPI interaction analysis

Question

[Liftedkris]

Hi fellows

I need to construct a dynamic PPI interaction analysis using gene expression data from three time points. I have this cytoscape app called DyNetViewer which requires me to put the data in a txt file before uploading it. I have my data in txt file but it gives error message “interrupted”. Who can suggest to me a cytoscape app for dynamic PPI analysis

Thanks

[Jean-Karim Heriche]

You should give more precision such as the full error message and an example of your data (could the format be unsuitable for this app?). I don't know this app but I would recommend to use R to analyze dynamic graphs as they can be represented as 3d arrays and gives access to more analysis options than what is prepackaged in a Cytoscape app. Also check this tutorial for how to visualize them.

[Liftedkris]

Please which R package can I use for that? Thanks

[Jean-Karim Heriche]

You can read graphs into an array using base R. Alternatively, graphs in R are often manipulated using the igraph package.

[Liftedkris]

Thanks so much. This should help