Network analysis "Cytoscape""?

More Shafeek Buhlak's questions See All

Could you please suggest to me an interesting and good book about Nanotechnology?

I want to know about nanotechnology from beginning to professional. Thus I want some book in this area

01 February 2021 2,266 13 View

Molecular sieves (testing and activating)

When we suspected that the molecular sieve needs replacement, there is a simple test if you don't know that your sample of molecular sieve is good or bad, there is a sample test that you can do...

01 January 1970 7,110 1 View

Which is the suitable protein-protein interaction data analysis method/platform for identification of targets from MS/MS?

I have a list of identifiers/hits processed based on log fold changes. I tried using pantherDB to generate GO terms and cytoscape for network construction. I need a clear picture on how to...

02 January 2024 8,770 2 View

How to change node-edge binding position in Cytoscape Desktop?

Dear colleagues, I am trying to plot a protein-protein interaction network in Cytoscape. My idea is to place the node representing the bait protein on one side of the figure, and on the other...

18 December 2023 9,182 2 View

Stepwise protocol on constructing target-pathway network using cytoscape. Particularly how to prepare pathway excel sheet?

Network Pharmacology

25 September 2023 6,202 1 View

How do I construct a target pathway interaction network on Cytoscape?

I need a stepwise protocol to construct target pathway interaction network on Cytoscape. How do I prepare the excel sheet?

10 September 2023 9,512 3 View

Cytoscape loading node error?

I was trying to use Cytoscape to replace IPA to fit our labs convenience, also with no self-generated database or profiles I feel the need to start with the Biogateway app, however whenever I...

03 July 2023 9,412 0 View

Does anyone had problems installing Cytoscape in Ubuntu 22.04.2 LTS?

I am trying to install Cytoscape in Ubuntu 22.04. I followed the instructions on the official website and installed Java 11, 17 and 18. None seems to work. I had this error every time: Error:...

30 May 2023 9,889 2 View

Hi everyone, why are my genes clustered like this in Cytoscape?

I want to visualize the common genes generated from the string database. When sent directly from the String database for visualization my genes are clustered so tightly that I can not tell which...

15 January 2023 4,002 1 View

How to mantain colours and to analyze merged networks in Cytoscape?

Dear All, I have a set of up- and downregulated miRNAs from which I have obtained two lists of possible up- or downregulated target genes (merging three online prediction databases). Of these...

19 May 2022 1,630 0 View

Why some proteins not in network?

I created a network using cytoscape and MINT. why is it so that although my protein of interest is interacting with other(literature search) but not in my network?

03 May 2022 6,415 1 View

How to identify bottleneck hub gene as potential drug target in cytoscape?

I have developed protein-protein network and define edge thickness based on combined-score in cytoscape. I am unable to identify bottleneck hub gene as drug target. I dont know how to use...

24 April 2022 4,324 0 View

Dipanka Tanu Sarmah

Its better to take any network from any paper .

Upload it on Cytoscape

And keep playing with the pluggins.

For a starter, use string pluggin

Giuseppe G. F. Leite

Dear Shafeek Buhlak

I strongly recommend that you look at the information Prof. Lars Juhl Jensen makes available on his website and also on his youtube channel.

Training Material:

https://jensenlab.org/training/#training-material

YouTube:

https://www.youtube.com/c/LarsJuhlJensen