Is there an alternative to Cytoscape software for building graphs from microarray data?
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6.4 years ago
vassialk ▴ 200

Is there an alternative to Cytoscape software for building graphs from the microarray data?

microarray software • 4.8k views
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6.4 years ago

You can use any number of other graph software as long as you can put your microarray data in a supported format. Examples are: BioLayout Express, gephi, GraphViz (with perl API).

EDIT: Since this has resurfaced, I'll add the igraph package for R.

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5.7 years ago

yes, you can use "NetworkAnalyst" which is designed to support integrative analysis of gene expression data through statistical, visual and network-based approaches.click to open network analyst

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5.7 years ago

ggnet2 a network visualization with ggplot2 (for R).

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5.7 years ago
Benn 8.2k

Or use R, since most analyses of microarrays are done in R: keep it in R. In R you can use e.g., Rgraphviz and graph packages.

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4.7 years ago
pengchy ▴ 450

Hi, you can try R, with the help of the book Statistical Analysis of Network Data with R

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