https://github.com/armbrustlab/thaps_catl

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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DOI references
Found 1 DOI reference(s) in README
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Scientific vocabulary similarity
Low similarity (5.7%) to scientific vocabulary

Last synced: 10 months ago · JSON representation

Repository

Created about 4 years ago · Last pushed about 4 years ago

Readme

GitHub page contiaing code for transcrtiptome processing described in paper

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

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)

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

Biological Oceanography Lab at the University of Washington