R scripts for the analysis of our RNAseq data

Code to accompany "Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress"

See our manuscript in BMC Genomics here

Information on files

• data_files: files needed for analysis are in this directory
• deseq2_drought: contains code for identifying differentially expressed genes and fold change figure
• drought_wgcna.R: contains code for WGCNA analysis, GO enrichment and heatmap figure
• pca.R: contains code for all PCAs and accompanying biplots
• transcript_info.R: contains code for identifying various stats about the transcripts (ie how many are only expressed in a certain condition).