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This article will explain in detail how to install and use the cytoscape-cytoHubba plug-in. The content of the article is of high quality, so the editor will share it with you for reference. I hope you will have a certain understanding of the relevant knowledge after reading this article.

Installation and use of cytoscape-cytoHubba plug-in

I. cytoHubba plug-in

1. Using the cytoHubba plug-in to assign values to each gene through the topological network algorithm, sorting and mining key genes (hub gene) and subnetworks

Degree

Edge Percolated component

Maximum neighborhood component

Density of Maximum Neighborhood Component

Maximal Clique Centrality

Six centralities (Botteleneck,EcCentricity,Closeness,Radiality,Betweenness, Stress)

CytoHubba ranks according to the attributes of nodes in the network. It provides 11 topology analysis methods, including:

two。 Download and install plug-ins

Search for the cytoHubba plug-in in cytoscape App Store (link: Cytoscape App Store) to download

Click Apps-App Manager, click install from file

Find the storage path of cytoHubba, open it and install it.

3.cytoHubba plug-in use

After opening cytoscape to import the network, click cytoHubba in Apps

1. First select the cytoHubba on the left to enter the work page

2. Select the network to be analyzed by target network

3. Click calculate

4. Click Top to adjust the number of key genes extracted according to the needs of your own project.

5. The Closeness below can be dropped down to select the calculation method.

6. Particular nodes: select the genes you are interested in for analysis (usually for the whole network analysis, this can be ignored)

5. Click on the bottom left: show the shortest path; show the first node to which hub gene is connected; show the longest subnetwork)

6. The list on the right shows the ranking of key genes: the darker the color, the higher the proof score, the more significant.

On how to achieve the installation and use of the cytoscape-cytoHubba plug-in to share here, I hope that the above content can be of some help to you, can learn more knowledge. If you think the article is good, you can share it for more people to see.

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