Questions tagged [graphs]

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Plant signaling pathway interconnections

I'm sorry for having such a juvenile question, but I'm still new in bioinformatics, and I was wondering whether there is any tool able to perform the task I'm dealing with now. Here is a short ...
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Can you style network visualizations of directed graphs using NETWULF?

I want to draw directed graphs using networkx, followed by manual tuning of the visualization with the use of NETWOLF. Here is the example of a network. ...
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How to group rarefaction curves by metadata

I'm trying to generate a rarefaction curve plot from a phyloseq object. I'm using the function ggrare using rarecurve function from the vegan package: The function rarecurve allow the ploting of all ...
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How to plot a graph of Linkage disequilibrium with limited information

I have a snp information in an excel file and I used SNPstat to do some analysis. But I also need a plot of LD for these snps. But my file is not formatted as the most programs required (.ped, hapmap, ...
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What are good resources to learn the basics of graph theory

I just spent half a day "debugging" a script that tried to get the betweenness centrality of a weighted graph with negative weights. However the package I used for that julia's ...