- /03_transcriptome_stomach_and_duodenum.R
- /04_script_nf-core_methylseq.sh
- /03_transcriptomics_stomach_and_duodenum.R
- /04_methylseq.genotoul.config

- /files/contrast ontologies/HRFI_fed_upr.csv
- /files/contrast ontologies/HRFI_upr.csv
- /files/contrast ontologies/HvsL_all.csv
- /files/contrast ontologies/LRFI_fasted_upr.csv
- /files/contrast ontologies/LRFI_fed_upr.csv
- /files/contrast ontologies/LRFI_upr.csv
- /files/contrast ontologies/Fasted_upr.csv
- /files/contrast ontologies/Fed_upr.csv
- /files/contrast ontologies/FvsFinH_all.csv
- /files/contrast ontologies/FvsFinL_all.csv
- /files/contrast ontologies/HRFI_fasted_upr.csv
- /files/contrast ontologies/FvsF_all.csv

- /files/metadata.txt
- /files/sample_sheet.csv
- /files/interesting ontologies/amigo_absorption_go_0050892_sscrofa_20230719.txt
- /files/interesting ontologies/amigo_gastric_acid_secretion_go_0001696_sscrofa_20230706.txt
- /files/interesting ontologies/amigo_lipase_go_0016298_sscrofa_20230719.txt
- /files/interesting ontologies/amigo_lipid_biosynthesis_go_0008610_sscrofa_20230719.txt
- /files/interesting ontologies/amigo_mucus_secretion_go_0070254_sscrofa_20230706.txt
- /files/interesting ontologies/amigo_stomach_development_go_0062094_sscrofa_20230706.txt
- /files/interesting ontologies/satiety_hormones.txt
- /files/metadata_stomach_and_duodenum.txt

- /plots/bonferroni_p_5pct/ACP C1-C2 LRFI.png
- /plots/bonferroni_p_5pct/ACP C1-C2.png
- /plots/bonferroni_p_5pct/ACP C1-C3.png
- /plots/bonferroni_p_5pct/Experimental_setup.png
- /plots/bonferroni_p_5pct/Plot CFAP20DC H-L, H-LinFas (2).png
- /plots/bonferroni_p_5pct/Plot CFAP20DC H-L, H-LinFas.png
- /plots/bonferroni_p_5pct/Plot gastrin.png
- /plots/bonferroni_p_5pct/Plot ghrelin.png
- /plots/bonferroni_p_5pct/Plot GULP1 Diff (2).png
- /plots/bonferroni_p_5pct/Plot GULP1 Diff.png
- /plots/bonferroni_p_5pct/Plot KLF11 F-F; F-FinH; F-FinL (2).png
- /plots/bonferroni_p_5pct/Plot KLF11 F-F; F-FinH; F-FinL.png
- /plots/bonferroni_p_5pct/Plot PTN H-LinFed (2).png
- /plots/bonferroni_p_5pct/Plot PTN H-LinFed.png
- /plots/bonferroni_p_5pct/ACP C1-C2 ellipses.png
- /plots/bonferroni_p_5pct/ACP C1-C2 HRFI.png

Plots for differential analysis with a multiple testing correction of 5% using Bonferroni

Inspired from the duodenum transcriptomic script.
Need files from nf-core/rnaseq with Salmon pseudoquantifications.
You will need to install several R packages.