GitHub - athieffry/Thieffry_et_al_2022_Plant_Cell: 🌱🧬 Collection of scripts for the paper: "PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave" (The Plant Cell 2022; PMID 35404429 🔗)

Code for the paper:
PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave. A Thieffry, D López-Márquez, J Bornholdt, MG Malekroudi, S Bressendorff, A Barghetti, A Sandelin, P Brodersen.
The Plant Cell 2022 - PMID:35404429

Non-obvious R requirements:

Name		Name	Last commit message	Last commit date
Latest commit History 10 Commits
data/RDS files		data/RDS files
1. CAGEfightR.R		1. CAGEfightR.R
10. DTU ANALYSIS.R		10. DTU ANALYSIS.R
11. LOCALISATION SIGNAL ANALYSIS.R		11. LOCALISATION SIGNAL ANALYSIS.R
12. uORF ANALYSIS.R		12. uORF ANALYSIS.R
13. PROTEIN DOMAINS.R		13. PROTEIN DOMAINS.R
14. non-adaptive ATI.R		14. non-adaptive ATI.R
2. CAGE TC-LEVEL DEA.R		2. CAGE TC-LEVEL DEA.R
3. ENHANCERS.R		3. ENHANCERS.R
4. CAGE HEATMAP T30.R		4. CAGE HEATMAP T30.R
5. CAGE GENE-LEVEL DEA.R		5. CAGE GENE-LEVEL DEA.R
6. TIMECOURSE DEGs CLUSTERING.R		6. TIMECOURSE DEGs CLUSTERING.R
7. PROMOTER SCANNING.R		7. PROMOTER SCANNING.R
8. RNA-seq HEATMAP.R		8. RNA-seq HEATMAP.R
9. ALTERNATIVE TSSs.R		9. ALTERNATIVE TSSs.R
README.md		README.md

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