Question: Is Ingenuity Pathway Analysis still relevant for analyzing RNA-seq data?
2
gravatar for jon.klonowski
14 days ago by
jon.klonowski30 wrote:

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

dataanalysis rna-seq ipa ngs • 162 views
ADD COMMENTlink modified 11 days ago by Morris_Chair120 • written 14 days ago by jon.klonowski30
1

has it ever been?

ADD REPLYlink written 11 days ago by Martombo2.5k
1

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

ADD REPLYlink written 11 days ago by Kevin Blighe45k
1
gravatar for arup
13 days ago by
arup1.5k
India
arup1.5k wrote:

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

ADD COMMENTlink written 13 days ago by arup1.5k

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 13 days ago by Kevin Blighe45k

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 13 days ago by arup1.5k

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 13 days ago • written 13 days ago by genomax69k
1
gravatar for Charles Warden
11 days ago by
Charles Warden7.0k
Duarte, CA
Charles Warden7.0k 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 11 days ago by Charles Warden7.0k
1
gravatar for Morris_Chair
11 days ago by
Morris_Chair120
Morris_Chair120 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 11 days ago by Morris_Chair120
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 11 days ago • written 11 days ago by genomax69k

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

ADD REPLYlink written 11 days ago by Morris_Chair120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 932 users visited in the last hour