multiDEG

R package to perform DEG analysis using Wilcox rank test, DESeq2, and edgeR methods

Installing

devtools::install_github("nicolau/multiDEG")

Loading dependencies packages

library(DESeq2)
library(edgeR)
library(tidyverse)
library(VennDiagram)

Loading example expression and phenodata files

data(raw.exp)
data(phenodata)

Calculating DEG using Wilcox, DESeq2, and edgeR methods

results <- DEG_analysis(raw.exp = raw.exp, phenodata = phenodata, treated = "INF", nontreated = "CTRL", class.column = "Class", adjust.method = "fdr", covariables = NULL, paired.samples.column = NULL)

Get Venn Diagram plot for overlap between three methods

For Up-regulated genes

plot(listDEGs = results, type = "up")

For Down-regulated genes

plot(listDEGs = results, type = "down")