Analyzing genes changed with diet in Fgf15-positive cells from ileum.
+-- data
+-- Run_2425
+-- Sample_113433
+-- ReadsPerGene.out.tab
+-- Sample_113434
+-- ReadsPerGene.out.tab
+-- ...
+-- Run_2425_seeley.csv
+-- Run_2643
+-- Sample_123057
+-- ReadsPerGene.out.tab
+-- Sample_123058
+-- ReadsPerGene.out.tab
+-- ...
+--
+-- Run_2643_seeley.csv
+-- genes.csv
+-- scripts
+-- analysis.R
+-- mapping.sh
+-- environment.yml
+-- README.md
- Create
anaconda
environment:conda env create -f environment.yml
- Activate
anaconda
environment:conda activate Fgf15
- Map FASTQ files:
bash scripts/map.sh
(note this does not work in the GitHub repo because FASTQ files are not included). - Analyze count files:
Rscript scripts/analyze.R
All results found in the results folder
- results.csv: numeric results from analysis pipeline
- kegg.csv: KEGG enrichment results
- plots/kegg.png: figure from the paper