dmfind - Network diffusion-based analysis of "omics" data for the identification of differentially enriched modules.

This tool implements functions for:

• performing network diffusion (also known as network propagation) of one or more vectors of gene-weights throughout an interactome of gene-gene interactions;
• defining ranked gene lists, where genes are prioritized according to the Network Smoothing Index (NSI), which is proportional to gene-weights and the network proximity of high gene-weights;
• assessing the characteristics of the (top) networks defined by the top ranked genes, based on proximity of high scoring genes, enrichment in high scoring genes, modularity and number of communities;
• obtaining the functional cartography of the top networks;
• comparing multiple networks by topology;
• visualizing the top networks and the relations between communities.

If you use this package please cite:

Bersanelli, M., Mosca, E., Remondini, D. et al. Network diffusion-based analysis of high-throughput data for the detection of differentially enriched modules. Sci Rep 6, 34841 (2016). https://doi.org/10.1038/srep34841

Installation

To install this package, start R and enter:

if (!requireNamespace("devtools", quietly = TRUE)){
  install.packages(devtools)
}
devtools::install_github("emosca-cnr/NPATools", build_vignettes=T)
devtools::install_github("emosca-cnr/dmfind", build_vignettes=T)

Documentation

Package vignettes are available at the URL: https://emosca-cnr.github.io/dmfind or can be visualized within R as follows:

library(dmfind)
browseVignettes("dmfind")