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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")
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.