Question: (Closed) GO enrichment tools
0
gravatar for restonpiston
6 months ago by
restonpiston30
restonpiston30 wrote:

Hello everyone! I have recently started to analyze RNA-seq data and I would like to know which tools are current now for the purpose of GO enrichment. I have checked out topGO, BiNGO, and building my own hypergeometric test, but none really satisfied me.

I am looking for suggestions of tools that do Gene Ontology Enrichment over a set of genes. I would like the tool to be able to receive a custom annotation and ontology, that enriches using the hypergeometric test and that does multiple test correction, FDR if possible. Any ideas of tools I haven't thought about?

Edit: topGO didn't really work for me as it doesn't work properly, and it made me create my own annotation packages. Also it lacked hypergeometric test, which is the test I think is the most suitable for my experiment. topGO was also lacking multiple test correction and the documentation was not good at all.

BiNGO worked perfectly, however it doesn't have a way to automate it, and I need that in order to integrate the tool in a pipeline.

go rna-seq R • 293 views
ADD COMMENTlink modified 6 months ago by EagleEye6.6k • written 6 months ago by restonpiston30

There are more than 400 GO tools available, it is impossible to suggest the right one, especially since they all come down to the same... If you want a more specific answer, please be more specific about what didn't satisfy with the tools you have used, and what would satisfy you and what you hope to find in other tools.

ADD REPLYlink modified 6 months ago • written 6 months ago by Benn7.9k

I have updated my answer, I was not very specific, you are right

ADD REPLYlink written 6 months ago by restonpiston30

Hello restonpiston!

We believe that this post does not fit the main topic of this site.

Found a tool that suited my needs

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 6 months ago by restonpiston30
3
gravatar for grant.hovhannisyan
6 months ago by
grant.hovhannisyan1.9k wrote:

Check clusterProfiler https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html

ADD COMMENTlink modified 6 months ago • written 6 months ago by grant.hovhannisyan1.9k

I checked it out, very nice tool, what I needed to be honest! The only disadvantage is that I had to unravel the obo file to annotate the genes also to the ancestors, but after doing so I could test enrichment and gene set quite easily.

ADD REPLYlink written 6 months ago by restonpiston30

glad to know. you might want to accept the answer then to close the thread.

ADD REPLYlink written 6 months ago by grant.hovhannisyan1.9k
0
gravatar for EagleEye
6 months ago by
EagleEye6.6k
Sweden
EagleEye6.6k wrote:

Check out Gene Set Clustering based on Functional annotation (GeneSCF)

ADD COMMENTlink written 6 months ago by EagleEye6.6k
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