<p>Answering this (3 years later) in case others stumble upon it.  Indeed the &quot;Analyze Network&quot; item in the &quot;Tools&quot; menu is the new version of NetworkAnalyzer. It is pre-installed with every release of Cytoscape now as a &quot;core app&quot; and provides degree and all the same centralities as the older version.</p>
<p>I suspect you ran into a temporary conflict between old and new versions (or with core vs user-installed apps).</p>

CC BY-SA 4.0
2024-05-02T16:54:22.607Z
2024-05-02T16:54:22.607Z
AlexanderPico
<p>I need to use NetworkAnalyzer to analyse the nodes of a PPI network on Cytoscape, but the pre-installed app is not displayed on the Tools menu.</p>
<p>I checked the App Manager, but it shows &quot;Installed&quot; beside the app name and also it is not in the Currently installed apps list, which is why I'm unable to perform uninstall-reinstall to fix it.</p>
<p>I've once replaced the app by installing it manually, but despite of that there's no change in the Tools menu.</p>
<p>There's an option &quot;Analyse Network&quot; in the Tools, probably a substitute of NetworkAnalyzer, but it is not showing the usual attributes (Degree, BetweenessCentrality etc) which are displayed on using Network Analyzer app.</p>
<p><a href="https://i.sstatic.net/r9q9j.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/r9q9j.png" alt="enter image description here" /></a></p>

<cytoscape>
How to activate an installed plugin (NetworkAnalyzer) on Cytoscape?
# How to activate an installed plugin (NetworkAnalyzer) on Cytoscape?

(Asked by: username_0 on 2021-06-06)

I need to use NetworkAnalyzer to analyse the nodes of a PPI network on Cytoscape, but the pre-installed app is not displayed on the Tools menu.

I checked the App Manager, but it shows "Installed" beside the app name and also it is not in the Currently installed apps list, which is why I'm unable to perform uninstall-reinstall to fix it.

I've once replaced the app by installing it manually, but despite of that there's no change in the Tools menu.

There's an option "Analyse Network" in the Tools, probably a substitute of NetworkAnalyzer, but it is not showing the usual attributes (Degree, BetweenessCentrality etc) which are displayed on using Network Analyzer app.

[![enter image description here](https://i.sstatic.net/r9q9j.png)](https://i.sstatic.net/r9q9j.png)

**Tags:** cytoscape

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## 1 answers

### Answer by username_1 on 2024-05-02. Score: 1

Answering this (3 years later) in case others stumble upon it. Indeed the "Analyze Network" item in the "Tools" menu is the new version of NetworkAnalyzer. It is pre-installed with every release of Cytoscape now as a "core app" and provides degree and all the same centralities as the older version.

I suspect you ran into a temporary conflict between old and new versions (or with core vs user-installed apps).


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