8.5 Reproducibility

The computational analysis of RNA-seq count tables demonstrated in this chapter require the following R library dependencies (only listing libraries outside of base R).

  • DESeq2: Differential expression analysis
  • RUVseq and EDASeq: Removing unwanted variation and diagnostics
  • gProfileR: Functional term enrichment analysis
  • Visualization:
    • ggplot2
    • ggfortify
    • pheatmap
    • corrplot
    • knitr

DESeq2, RUVSeq, and EDASeq can be installed from the Bioconductor repository via:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install(c('DESeq2', 'RUVSeq', 'EDASeq'))

The remaining package can be installed from CRAN via:

install.packages(c('gProfileR', 'ggplot2', 'ggfortify', 'pheatmap', 'corrplot', 'knitr'))