Bulk RNA-seq analyses in R

The code parses the files and produces the following plots and analyses that can be used as paper-ready figures:

• Volcano plot
• MA plot
• PCA
• Heatmap
• Faceted boxplots
• Pathway analysis

Example figures:

Table of contents:

• Parsing function
• save.png function
• save.emf function
• Volcano plot function
• MA plot function
• PCA function
• Heatmap function
• Faceted boxplots function
• Pathway analysis function

Required files:

4 files

• em: a normalised expression matrix
• de: differential expression statistics between each sample group of interest
• annotation: genome annotation
• ss: sample group information.

Required installation of the following R libraries:

library(ggplot2)

library(reshape2)

library(ggrepel)

library(tidyverse)

library(amap)

library(devEMF)

library(clusterProfiler)

library(org.Hs.eg.db)

library(enrichplot)

library(GOSemSim)

library(DOSE)