Gene set enrichment analysis tools

Question

[niutster]

Hi

I am looking for a tool in R that do a good Gene set enrichment analysis. Can anybody help?

[WouterDeCoster]

Hi niutser,

Googling "gene set enrichment R" already gives plenty of hits! It's recommended to search first and then ask questions.

Cheers,
Wouter

[EagleEye]

Hi WouterDeCoster,

I feel it is good to discuss with bioinformatics people to start with enrichment analysis. There are lot of enrichment analysis tools available, it is important to know how far those tools are updated with their database/information. For example this article talks about the issue in using outdated resource for enrichment analysis,

Impact of outdated gene annotations on pathway enrichment analysis

[WouterDeCoster]

You are definitely right, and it's indeed likely that with the myriad of available tools OP would not find "the best" (if a tool like that exists). I also think the question has to be asked and discussed. But I would like to encourage pro-active searching.

The question would show a lot more effort if it would start like "I searched for gene set enrichment analysis tools in R and found 86 different tools and I'm not sure which one is the most appropriate for my analysis using RNA-seq on human data of 32 cystic fibrosis patients compared with 12 control individuals. (...) (...)"

[EagleEye]

It is true that for enrichment analysis, the question should be asked in detail and more specific and also has to be extensively investigated about the resource it uses. This is the topic which has to to discussed extensively. Rather than selecting a tool which is convenient to use, one has to think is that tool worth to looking at. Some people just blindly choose any enrichment tools which does the job.

Three years back when I raised this issue in our lab, nobody was believing since the tool they where using had huge number of citations (as you know which tool I am talking about). They did not realize that it will have profound effect on the results. That was the reason I started designing my own tool to retrieve current data from the database and perform enrichment analysis. Now they realize the difference in using outdated and most up-to-date resource in their analysis.

Answer 1

[EagleEye]

Gene Set Clustering based on Functional annotation (GeneSCF) With real-time enrichment analysis. Sorry but not in R.

Answer 2

[Chirag Parsania]

Hi,

There are so many GSEA tools. GSEA is one of them. Other than I like following two 1) topGO 2)Bingo