What's the best software to build a pathway using your own -omics datasets?

Question

[moxu]

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

Thank you!

[Medhat]

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?

[moxu]

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.

[moxu]

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 !

[WouterDeCoster]

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.

[moxu]

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

Answer 1

[Ron]

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

http://www.circos.ca

[moxu]

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.

[Ron]

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