Thaps_Catl

GitHub page contiaing code for transcrtiptome processing described in paper

"Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana"

Code files:

• WGCNA.R: Script that runs WGCNA clustering.
• GLM_DE.R: Script that does differential expression analysis using EdgeR.
• enrichment.R: Script that performs functional enrichemnt on genes in WGCNA modules and differentially expressed genes for the three time comparisons.

R version used: R version 4.1.0 (2021-05-18)

Instructions for running scripts:

1. Download all data .csv files from Zenodo (10.5281/zenodo.6672614). There are 5 data files needed for the code to run: all_abundance_TPM.csv, DE.csv, Experimental_parameters.csv, thaps_GO.txt, WGCNA_network.csv
2. Create a folder on your desktop called Thaps_Catl, and save all files and code into that folder (~/Desktop/Thaps_Catl).
3. Open code in R and run scripts.