Question: Is Ingenuity Pathway Analysis still relevant for analyzing RNA-seq data?
2
gravatar for jon.klonowski
14 months ago by
jon.klonowski70 wrote:

Is Ingenuity Pathway Analysis still relevant for analyzing RNA-seq data? Are there better alternatives out there?

dataanalysis rna-seq ipa ngs • 1.0k views
ADD COMMENTlink modified 14 months ago by Morris_Chair200 • written 14 months ago by jon.klonowski70
1

has it ever been?

ADD REPLYlink written 14 months ago by Martombo2.6k
1

Better than other commercial products. I have no relationship to Qiagen, for the record.

ADD REPLYlink written 14 months ago by Kevin Blighe65k
1
gravatar for Arup Ghosh
14 months ago by
Arup Ghosh2.7k
India
Arup Ghosh2.7k wrote:

IPA is used for pathway analysis, there is some other premium software available like GeneGo MetaCore, Advaitabio pathway analysis.

ADD COMMENTlink written 14 months ago by Arup Ghosh2.7k

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.

ADD REPLYlink written 14 months ago by Kevin Blighe65k

They are still in the market because of some of the group leaders thinks a particular pathway term can get their articles published.

ADD REPLYlink written 14 months ago by Arup Ghosh2.7k

If you subject area is well covered by IPA then it can literally save you months of PubMed work. It is also a general resource for building hypotheses using interactions encoded in their database, even if you don't have any data of your own.

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax90k
1
gravatar for Charles Warden
14 months ago by
Charles Warden7.9k
Duarte, CA
Charles Warden7.9k wrote:

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:

https://changlab.uth.tmc.edu/gather/

ADD COMMENTlink written 14 months ago by Charles Warden7.9k
1
gravatar for Morris_Chair
14 months ago by
Morris_Chair200
Morris_Chair200 wrote:

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

ADD COMMENTlink written 14 months ago by Morris_Chair200
1

While you can create a free account (and possibly do some limited analysis) this software is not free. See FAQ for additional details (Do you offer a free trial section).

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax90k

Oh pardon, I used for a short time in the past and I thought was free, thank you genome

ADD REPLYlink written 14 months ago by Morris_Chair200
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