Each directory contains an R script with the same name as the folder. The subdirectory data/ typically contains any required input data and (often) a .RData file containing the R environment after the script has run. See comments in each R file for details.
Find genes in RNA-Seq data that are differentially expressed in IPF versus Normal conditions using DESeq.
Find exonic regions in RNA-Seq data that are differentially used in IPF versus Normal conditions using DEXSeq.
Download microarray data from GEO, find differentially expressed genes, and compare to RNA-Seq data.
Determine whether GWAS genes are enriched for differential expression.