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Florent-1 / Molecular-Networks-from-Compound-Discoverer-to-Cytoscape

Contain a R script to make to data file of a molecular network generated by Compound Discoverer to a reable format for Cytoscape.
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Where did the "Nodes" and "Links" javascript files come from? #1

Open ijgretch opened 5 days ago

ijgretch commented 5 days ago

Hi! I ran a network in CD and would love to export it to cytoscape or another tool with more options for customized viewing. I would love to use your script, I am just wondering where/how the input files you use are generated. When I look at the output generated by CD, there are many .js files, but none named "nodes" or "links". Thanks!

Florent-1 commented 21 hours ago

Hi, you first need to get the "data.js". This file is composed of three parts, if you search there you should be able to find the information about "nodes" and "links". Otherwise, I will try to update more information during the next week, just let me know if you need it or not please. Also among the two scripts that are available, you should start, in a first time with : Script data Molecular Network from CD to Cytoscape.R

ijgretch commented 4 hours ago

Thanks!! Your script worked like a charm and you are a hero of the internet.

-Gretchen Johnson, MS (she/her)

PhD student | Kubanek Lab

Ocean Sciences and Engineering Program

Georgia Institute of Technology

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From: Florent-1 @.> Sent: Sunday, November 17, 2024 3:04 PM To: Florent-1/Molecular-Networks-from-Compound-Discoverer-to-Cytoscape @.> Cc: Johnson, Gretchen @.>; Author @.> Subject: Re: [Florent-1/Molecular-Networks-from-Compound-Discoverer-to-Cytoscape] Where did the "Nodes" and "Links" javascript files come from? (Issue #1)

Hi, you first need to get the "data.js". This file is composed of three parts, if you search there you should be able to find the information about "nodes" and "links". Otherwise, I will try to update more information during the next week, just let me know if you need it or not please. Also among the two scripts that are available, you should start, in a first time with : Script data Molecular Network from CD to Cytoscape.R

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