Scripts

Script Name Packages
Step1_TxImport.R tximport, tidyverse, biomaRt, ensemblDB
Step2_dataWrangling.R ggplot2, tidyr, matrixstats, edgeR
Step3_multivariate.R ggplot2, tidyverse, plotly, gt, DT
Step4_publicData.R rhdf5
Step5_diffGenes.R limma, edgeR, SVA
Step6_modules.R gplots, Rcolorbrewer, heatmaply, d3heatmap
Step7_functionalEnrichment.R GSVA, gprofiler2, clusterProfiler, msigdbr, enrichplot
Rmarkdown_template.Rmd, Rmarkdown_essentials.Rmd, flexdashboard_essentials.Rmd Rmarkdown, Knitr, renv, flexdashboard
buildPkg.R devtools, usethis, roxygen2