Gene Regulatory Network (GRN) reconstruction and assessment tools

Question

[Parisa]

Hi,

I am looking for tools and algorithms about GRN reconstruction as well as GRN assessment. Some examples are CellNet, ARACNE, TIGRESS, and so on. I wonder if anybody here has any suggestion.

Thank you in advance.

[zizigolu]

in genepattern (pathway analysis), there are ready toold that only need the input file and assessment part also is in downstream part.

i found NetBenchmark package also doing GRN inference and evaluation on more than 10 methods but i could not figure out that yet. but this package failed to evaluate the results.

Answer 1

[k.theofilatos]

You can construct co-expression networks from your gene expression experiments with several algorithms and methods with InSyBio BioNets (a demo is available here and you can request for a free one month access at [e-mail]). For more details read the relevant white paper: http://insybio.com/pages/bionets