network software

=> RTN, bioconductor

https://bioconductor.org/packages/release/bioc/html/RTN.html

=> KEGGREST
http://bioconductor.org/packages/release/bioc/vignettes/KEGGREST/inst/doc/KEGGREST-vignette.R


=> Cytoscape


=> KENev



=> MARINa (MATlab)

=> ingenuity

=> geneXplain

Tools for network anlysis

cytoscape

clustering

NEAT
http://rsat.ulb.ac.be/index_neat.html

MCL

weka,

MATLAB

R igraph

elki