Is Ingenuity Pathway Analysis still relevant for analyzing RNA-seq data? Are there better alternatives out there?
•
written
by
jon.klonowski
IPA is used for pathway analysis, there is some other premium software available like GeneGo MetaCore, Advaitabio pathway analysis.
I agree. People are still very much using it (I am not, though). It is one of those bioinformatics commercial products that appears to be surviving quite nicely alongside the open source packages. People publish results using it, too.
They are still in the market because of some of the group leaders thinks a particular pathway term can get their articles published.
While you can't guarantee that IPA will work for any given project, I think it is often useful. However, I think having access to open-source alternatives is very important (sometimes as a replacement for some projects, sometimes as a complement to extend understanding for other projects).
I think the website is currently encountering some issues during an upgrade, but I would usually recommend Enrichr:
https://amp.pharm.mssm.edu/Enrichr/
You may also find GATHER results to be useful:
I'm not a fun of this tools but I guess a similar (free) alternative is this:
https://advaitabio.com/ipathwayguide/
you can find a well explained tutorial on youtube
Oh pardon, I used for a short time in the past and I thought was free, thank you genome
Log in to answer this question.
has it ever been?
Better than other commercial products. I have no relationship to Qiagen, for the record.