Is there an alternative to Cytoscape software for building graphs from the microarray data?
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.
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
a network visualization with ggplot2 (for R).
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.
Hi, you can try R, with the help of the book Statistical Analysis of Network Data with R
This link looks very suspicious to me.
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