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The multiDEGGs package test for differential gene-gene correlations across different groups of samples in multi omic data.
Specific gene-gene interactions can be explored and gene-gene pair regression plots can be interactively shown.

Install from CRAN:
install.packages("multiDEGGs")

Install from Github:
devtools::install_github("elisabettasciacca/multiDEGGs")

Load package and sample data

library(multiDEGGs)  data("synthetic_metadata")  data("synthetic_rnaseqData")  data("synthetic_proteomicData")data("synthetic_OlinkData")

Generate differential networks:

assayData_list<-list("RNAseq"=synthetic_rnaseqData,"Proteomics"=synthetic_proteomicData,"Olink"=synthetic_OlinkData)deggs_object<- get_diffNetworks(assayData=assayData_list,metadata=synthetic_metadata,category_variable="response",regression_method="lm",padj_method="bonferroni",verbose=FALSE,show_progressBar=FALSE,cores=2)

Visualise interactively (will open a shiny interface)

View_diffNetworks(deggs_object)

Get a table listing all the significant interactions found in each category

get_multiOmics_diffNetworks(deggs_object,sig_threshold=0.05)

Plot differential regression fits for a single interaction
plot_regressions(deggs_object, assayDataName = "RNAseq", gene_A = "MTOR", gene_B = "AKT2", legend_position = "bottomright")

citation("multiDEGGs")