Question: miRNA-target network construction packages in R and Bioconductor ??
1
gravatar for unique379
4.0 years ago by
unique37970
Spain
unique37970 wrote:

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.

 

bioconductor R • 2.5k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by unique37970

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?

ADD REPLYlink written 4.0 years ago by Sean Davis25k
1
gravatar for Sean Davis
4.0 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

Take a look at:

http://igraph.org/r/

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

Bioconductor Rgaphviz package

 

ADD COMMENTlink written 4.0 years ago by Sean Davis25k

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

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by unique37970

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.

 

ADD REPLYlink written 4.0 years ago by Sean Davis25k
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