miRNA-target network construction packages in R and Bioconductor ??
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9.1 years ago
unique379 ▴ 110

Dear all,

I have list of miRNAs and their associated target genes and would like to create miR:gene Network. is their any best packages in R and Bioconductor to create such a graph? I want to make a graph like this:

Please help.

Thank you.

R Bioconductor • 4.0k views
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What do you mean by "graph"? If you already have the miRNAs and their targets, what else is it that you would like to do?

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9.1 years ago

Take a look at:

http://igraph.org/r/

http://christophergandrud.github.io/networkD3/

Bioconductor Rgaphviz package

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Millions of thanks Davis for networkD3 package, its really cool. Just let me know, what is the difference between "networkD3" and "d3Network" package ??

link: http://christophergandrud.github.io/d3Network/

I install both and testing now but d3Network does not work for me. Down know what wrong with that, while running function with required input, it prints only source code of particular function in R terminal.

like:

d3SimpleNetwork(networkData, height = 300, width = 700,fontsize = 15)

!DOCTYPE html>
        <meta charset="utf-8">
        <body>
 <style>
.link {
stroke: #666;
opacity: 0.6;
stroke-width: 1.5px;
}
.node circle {
stroke: #fff;
opacity: 0.6;
stroke-width: 1.5px;
}
text {
font: 7px serif;
opacity: 0.6;
pointer-events: none;
}
</style>

.....bla bla bla
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d3Network is not being maintained anymore. networkD3 is the package to use....

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d3Network is not being supported anymore. The author is now supporting networkD3, so you should use that instead. If you would like to report a bug in software, it is best to report it to the author rather than here.

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