This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Is there a tutorial on pathway enrichment analysis in R without ready-made packages?

Hi all,

I would like to run a pathway enrichment analysis using a gene list as the input without existing packages. I have searched for some articles but they are about how to use particular software. I was wondering what is an accepted workflow or algorithm in pathway enrichment analysis after retrieving data from the database.

Thanks.

r pathway enrichment analysis
• 2,522 views • link
updated by kinalimeric • kinalimeric • written by wuqingkuangsha • wuqingkuangsha

without existing packages.

But why?

• 0 views • link
written by WouterDeCoster WouterDeCoster

There are actually many tools but someone's interest organism is might not be covered by these tools. I am interested in figuring out this stuff myself

• 0 views • link
written by wuqingkuangsha • wuqingkuangsha

someone's interest organism is might not be covered by these tools

There are many tools that will work for any organism.

I am interested in figuring out this stuff myself

If you have already found some tools, check their source code, which should be available for most of them.

• 0 views • link
written by igor igor

1 answer

You can perform a hypergeometric test by yourself.

• 0 views • link
written by kinalimeric • kinalimeric

Log in to answer this question.

More posts like this