You can find the data and algorithms/scripts employed by PlaNet here.

Co-expression networks/expression data:
Readme file describing the networks/expression data
Arabidopsis thaliana co-expression network
Hordeum vulgare co-expression network
Medicago truncatula co-expression network
Populus sp. (poplar) co-expression network
Oryza sativa (rice) co-expression network
Glycine max (soybean) co-expression network
Nicotiana tabacum (tobacco) co-expression network
Triticum spp. (wheat) co-expression network
Physcomitrella patens co-expression network

Additional data:
Conserved and duplicated modules (Physcomitrella patens vs. Arabidopsis thaliana and Oryza sativa)

Scripts:
Python implementation of Heuristic Cluster Chiseling Algorithm (HCCA) 
Python implementation of PlaNet