R packages

wTO

wTO: Computing Weighted Topological Overlaps (wTO) & Consensus wTO Network

Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks (Nowick et al. (2009) <doi:10.1073/pnas.0911376106>) 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). Read more

CoDiNA

Co-Expression Differential Network Analysis: CoDiNA

The usage of the Co-expression Differential Network analysis has been growing by the Biological and Medical science for the analysis of complex systems or diseases. We have developed a method that is able to compare as many networks as desired, by caracterizing both links and nodes that are common, different or specific to each network. More information can be found at [arXiv:1802.00828]. Read more

RichR

RichR: Enrichment for Diseases in a Set of Genes

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. Read more