7.1 Fetch workshop files

7.1.1 Download files from GitHub repository

We will copy locally a few files prepared for the workshop. Please copy-paste the following block of commands in the R console:

# list of files to download
ls_files <- c("DEG_counts.csv", "DEG_counts_sample.csv", "DEG_counts_sample.xlsx", "metadata.csv", "DEG_counts_sample_long.csv", "gencode.vM38.annotation_sample.csv", "counts_100genes.csv")

# create local directory where files will be stored
local_dir <- "GSE277039"
dir.create(local_dir, showWarnings = F)

# loop through the list of files to download them locally
for(i in ls_files){
  download.file(file.path("https://raw.githubusercontent.com/sarahbonnin/SteppingStone2026_IDIBAPS_RDataViz/master/GSE277039/", i), file.path(local_dir, i))
}

7.1.2 Dataset description

For this course, we will use gene expression data from GSE277039 Gene Expression Omnibus (GEO) dataset.

“…bulk RNA sequencing of primary keratinocytes isolated from wild-type and Pla2g4d-deficient mice and studied transcriptional changes under basal and cytokine stimulation.”

For simplicity, we only used wild-type (WT) and Pla2g4d-deficient (KO) samples from the experiment, and calculated a simple pairwise differential expression between KO and WT.