runTest.R

# if (!require("BiocManager", quietly = TRUE))
#   install.packages("BiocManager")
# 
BiocManager::install(c("airway", "DESeq2","SummarizedExperiment"
                       ,"GenomicRanges"
                       ,"IRanges"
                       ,"S4Vectors"
                       ,"pcaExplorer"
                       ,"IHW"
                       ,"goseq"
                       ,"limma"
                       ,"GOstats"
                       ,"GO.db"
                       ,"AnnotationDbi"
                       ,"BiocParallel"
                       ,"BiocStyle"
                       ,"airway" , "apeglm", "ashr"
                       ,"org.Hs.eg.db"
                       ,"TxDb.Hsapiens.UCSC.hg38.knownGene"
                       ,"DEFormats"
                       ,"edgeR"))
install.packages('shinyjqui')
install.packages("markdown")

library(idealImmunoTP)
library(airway)


library(DESeq2) 
library(SummarizedExperiment) 
library(GenomicRanges) 
library(IRanges)
library(S4Vectors) 
library(ggplot2) 
library(heatmaply)

library(plotly)
library(pcaExplorer) 
library(IHW) 
library(gplots) 
library(UpSetR) 
library(goseq) 
library(stringr) 
library(dplyr)
library(limma) 
library(GOstats) 
library(GO.db) 
library(AnnotationDbi) 
library(shiny)
library(shinydashboard) 
library(shinyBS) 
library(DT) 
library(rentrez) 
library(rintrojs) 
library(ggrepel) 
library(knitr)
library(rmarkdown) 
library(shinyAce) 
library(BiocParallel) 
library(grDevices) 
library(base64enc)
library(methods)
library(testthat) 
library(BiocStyle) 
library(airway) 
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg38.knownGene) 
library(DEFormats) 
library(edgeR)

load(file = "testData.RData")

idealImmunoTP(dds_obj = dds_airway, annotation_obj = annotation_airway, res_obj = res_airway)