Question: What's the best software to build a pathway using your own -omics datasets?
1
gravatar for moxu
4.2 years ago by
moxu470
moxu470 wrote:

There are tons of software products out there to build gene-gene network and/or pathway. Which one is the most popular?

Thank you!

algorithm • 904 views
ADD COMMENTlink modified 4.2 years ago by Ron1.0k • written 4.2 years ago by moxu470

there is a lot of definitions for best, it could be speed, accuracy or both at the same time I think it all depends on what you have and what you need to achieve.

for example look to the answe of this question

Which Is The Best Software To Represent Biological Pathways In A Directed Graph (Network) ?

can you decide what is the best from answers of the previous question?

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Medhat8.8k

Thanks for the reply. The post looks interesting, but it's 6 years ago. :) Away too old.

By best, I mean best quality -- least false positives & least false negatives.

ADD REPLYlink written 4.2 years ago by moxu470

You are right,, I'm interested in deriving a pathway. The actual types of data do not really matter, right? They can be gene expression, proteomics, ChlP, ... Mathematically they are all just numbers.

Thank you !

ADD REPLYlink written 4.2 years ago by moxu470

Based on comment below I interpreted that you want to derive a pathway from some type of data (and not visualization). You should probably tell us which data you have on which a pathway should be based.

ADD REPLYlink written 4.2 years ago by WouterDeCoster44k

As I said in the title --omics data such as gene expression profiles, porteomics datasets, ChIP & etc.

ADD REPLYlink written 4.2 years ago by moxu470
0
gravatar for Ron
4.2 years ago by
Ron1.0k
United States
Ron1.0k wrote:

You can try Circos.it lets you modify the code and do your own customizations.

http://www.circos.ca

ADD COMMENTlink written 4.2 years ago by Ron1.0k

Thanks. It's a very nice tool, but it only visualises pathways. I would like to generate pathways based on information (such as gene expression, histone modification, etc.) of genes.

ADD REPLYlink written 4.2 years ago by moxu470

Check out this post . Which program, tool, or strategy do you use to visualize genomic rearrangements?

ADD REPLYlink written 4.2 years ago by Ron1.0k
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: 1520 users visited in the last hour