Question: Network construction methods using Bayesian Network or mutual information
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gravatar for zhang.jianhai
4 weeks ago by
zhang.jianhai0 wrote:

Hello,

I want to use Bayesian Network (BN) or Mutual Information (MI) based R packages to construct gene network. I have checked BNArray and CLR, but it seems they are not available on CRAN or Bioconductor, and there is no detailed tutorial to follow, so does anyone know other BN or MI based R packages with available tutorials for gene network construction?

If they are able to identify gene network modules/clusters, it would be best, since my final target is to identify gene clusters/modules.

Thanks in advance.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by zhang.jianhai0

If you upload your normalized gene expression data (genes are in rows and samples in columns) in cytoscape, there is network option in menu to infer a regulAtory network by information theory or whatever.hereafter in cytoscape there is a plugin app named moduland by which you can infer interconnected nodes in your network as gene modules.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by F3.4k

Thanks for your reply. The Cytoscape may work out, but I want R-based methods since I have many samples and want to write a program to automatically identify gene modules. If I use Cytoscape I have to manually input those samples, and it is not convenient in the long-term.

ADD REPLYlink written 4 weeks ago by zhang.jianhai0

Minet r package infers the network just by two lines of code. But after building the network easiest way is importing network to cytoscape to use moduland app

ADD REPLYlink written 4 weeks ago by F3.4k
1
gravatar for Kevin Blighe
4 weeks ago by
Kevin Blighe39k
Republic of Ireland
Kevin Blighe39k wrote:

My own tutorial is based on igraph and is actually quite similar to many other published network analysis methods: Network plot from expression data in R using igraph

At least by following that tutorial, you will understand what is happening to your data. With other tools, the process can be heavily automated.

Also, there is a MatLab program called CGBayesnets, written by a colleague of mine.

ADD COMMENTlink written 4 weeks ago by Kevin Blighe39k
1

Thanks Kevin, I like your tutorials a lot because line by line guiding beginners among which I really liked your posts on machine learning (modelling). I also appreciate your package to drawing volcano plot

ADD REPLYlink written 4 weeks ago by F3.4k

You are welcome, F

ADD REPLYlink written 4 weeks ago by Kevin Blighe39k
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