Question: Clustering Analysis In Gene Coexpression Network
0
gravatar for Ane
6.3 years ago by
Ane180
Ane180 wrote:

Hello!

I have a gene coexpression network and i want to analyse and visualize the clusters of the network (i.e show different clusters in different colours). I have used R studio and cytoscape for the network construction and analysis, so far. Although i have managed to define the modules of the network with different algorithms, i couldn't find a proper way to visualize the clusters. Cytoscape plugins Glay and ClusterMaker seemed very helpful but unfortunately they are not compatible with cytoscape 2.8.

Could you recommend similar cytoscape plugins, r packages and/or any other software for this kind of analysis?

Thanks in advance, Ane

gene-expression clustering • 3.3k views
ADD COMMENTlink modified 6.3 years ago by Arnaud Ceol840 • written 6.3 years ago by Ane180

"used R studio" - Rstudio is an R IDE, so this does not tell us what you did. Did you use an R package?

ADD REPLYlink written 6.3 years ago by Neilfws48k

yes, i used igraph and i have imported it into cytoscape with graphml plugin

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Ane180
1
gravatar for Arnaud Ceol
6.3 years ago by
Arnaud Ceol840
Milan, Italy
Arnaud Ceol840 wrote:

I'm using ClusterMaker with Cytoscape 2.8 without problem. Once you have created the cluster, a button appears allowing you to visualize them.

ADD COMMENTlink written 6.3 years ago by Arnaud Ceol840

i was trying to install a previous version! i created the clusters with mcl algorithm and managed to visualize them, too! Is there any way to visualize them in different colours in the same network?

ADD REPLYlink written 6.3 years ago by Ane180

The answer comes quite late, but maybe it still can be useful for someone. When you create the clusters, there is an advanced Cytoscape option to generate metanodes. An attribute will be added to each node that you can use to colour the clusters.

ADD REPLYlink written 6.2 years ago by Arnaud Ceol840
0
gravatar for Leandro Lima
6.3 years ago by
Leandro Lima930
San Francisco, CA
Leandro Lima930 wrote:

Hello, Ane!

Maybe this post can help you.

gene coexpression networks

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Leandro Lima930
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