Question: How to compare gene clusters of non-model organisms using clusterProfiler package?
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gravatar for Agamy89
2.6 years ago by
Agamy890
Agamy890 wrote:

Hi everyone,

I am doing a transcriptomic analysis of a particular fungus according to pH change. I have determined DEG and enriched GO using topGO Package (as the genus I am working with is a non-model organism and I have to use my own GO annotation file). Next, I have done soft clustering in order to figure out which genes clusters are increased and decreased, respectively, using fuzzy soft clustering. I have successfully done it and figured out the GO of each cluster as well, but visualizing GO of each cluster is laborious and time-consuming. Furthermore, the resulted graphs will be confusing and uninformative. I have seen the clusterProfiler package and find out that there is a possibility to compare GO of several gene clusters in one graph. This will be a perfect graph for visualizing GO of all clusters I have. However, I find difficulty to understand how the tutorial is working. As I understand, the package works well with model organisms only. Also, it did not accept the output of other GO packages like topGO for example. If I am wrong, I will be thankful for anyone can guide me the proper way to visualize the data using clusterProfiler or other packages can give me a similar graph.

The image is shown in this like under the title (Visualization of profile comparison)

https://bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

Thank you in advance

ADD COMMENTlink modified 2.5 years ago by Biostar ♦♦ 20 • written 2.6 years ago by Agamy890
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