Ileum organoids grown under hypoxic and normal oxygen conditions

Methodology

• This repository hosts the souce code used to analyze the data from the paper - XXX
• The companion website for this paper is hosted here

Scripts

All script can be found in the /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_multiQC.sh - Script to perform QC analysis of raw reads and alignment statistics
3. /src/03_downloadGenomes.sh - Download the hg38 reference genome from Ensembl
4. /src/04_indexRsubread.R - Indexing of the reference genome
5. /src/05_alignmentRsubread.R - Script to perform read alignment analysis on the raw fastq files using Rsubread
6. /src/06_countsRsubread.R - Script to count reads overlapping genes
7. /src/07_postProcessing.R - Script to preprocess and filter the raw count data
8. /src/08_exploratoryAnalysis.R - Script to perform various Exploratory analysis
9. /src/09_DSeq2Analysis.R - Script to perform Differential gene expression analysis (DGE) using DSeq2
10. /src/09_DSeq2_Rmarkdown/ - Script to visualize the results of Dseq2 as interactive data tables
11. /src/10_differentialGeneExpression.R - Script to analyze DGE results focusing on specific genes of interest
12. /src/11_enrichmentAnalysis.R - Script to perform Enrichment analyses
13. /src/12_plotGeneModulesExpression.R - Script to plot the expression of Hypoxia, EMT and WNT signalling genes
14. /src/13_computeCellFractions.R - Using CIBERSORTx to identify Ileum cell types using single-cell data