Calculates network measures such as Largest Connected Component (LCC), Proximity, Separation, Jaccard Index, along with permutation, when needed.

Categorize links and nodes from multiple networks in 3 categories: Common links (alpha) specific links (gamma), and different links (beta). Also categorizes the links into sub-categories and groups. The package includes a visualization tool for the networks. More information about the methodology can be found at https://doi.org/10.1371/journal.pone.0240523

It provides a list of genes associated to diseases (g2d$clean and g2d$complete) based on the following 4 publications (GS2D, Fontaine (2016) doi:10.18547/gcb.2016.vol2.iss1.e33, DisGeNET, Pinero (2016) doi:10.1093/nar/gkw943 Berto2016, Berto (2016) doi:10.3389/fgene.2016.00031 and PsyGeNET, Sacristan (2015) doi:10.1093/bioinformatics/btv301). Those lists were combined and manually curated to have matching disease names. When provided a list of gene names, it calculates the disease enrichment of the gene set. The enrichment is calculated using proportion test and Fisher’s exact test. Adjusted fdr p-values are returned alongside with p-values combined using the Fisher’s method.

Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks.