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))
install.packages("BiocManager")
BiocManager::install(c('DESeq2', 'RUVSeq', 'EDASeq'))
The remaining package can be installed from CRAN via:
install.packages(c('gProfileR', 'ggplot2', 'ggfortify', 'pheatmap', 'corrplot', 'knitr'))