T84 cell treated with IL22 and IFNL

• This repository hosts the source code used to analyze the transcriptomic profiling data (RNAseq) from the paper - IL-22 promotes cell proliferation to combat virus infection in human intestinal epithelial cells
• The companion website for this paper is hosted here

Scripts

All scripts are located in /src/ directory

0. /src/00_submitJobs.sh - This is the bash script to run analysis 1,2,3,4 in the cluster environment
1. /src/01_fastQC.sh - Script to perform fastQC analysis on the raw fastq files
2. /src/02_alignmentRsubread.R - Script to perform read alignment analysis on the raw fastq files using Rsubread
3. /src/03_countsRsubread.R - Script to count reads overlapping genes
4. /src/04_multiQC.sh - Script to perform QC analysis of raw reads and alignment statistics
5. /src/05_postProcessing.R - Script to preprocess and filter the raw count data
6. /src/06_exploratoryAnalysis.R - Script to perform various `Exploratory analysis
7. /src/07_DSeq2Analysis.R - Script to perform Differential gene expression analysis (DGE) using DSeq2
8. /src/07_DSeq2_Rmarkdown/ - Script to visualize the results of Dseq2 as interactive data tables
9. /src/08_differentialGeneExpressionAnalysis.R - Script to analyze DGE results focusing on specific genes of interest
10. /src/09_enrichmentAnalysis.R - Script to perform Enrichment analyses
11. /src/10_plotGeneModulesExpression.R - Script to plot the expression of JAK-STAT, IL22 and IFN-L signaling genes