Module 0 · Setup (before the day)

1. Install R ≥ 4.3 from CRAN and RStudio from posit.co.
2. Download this transcriptomics tutorial folder and keep the folder structure as it is.
3. Open RStudio, set the working directory to the workshop folder, and run:

r source("scripts/00_install.R")

It installs DESeq2, piano, fgsea, pheatmap and ggplot2 from Bioconductor/CRAN, and finishes with "All packages are installed". On Windows, if R asks to install from source, answer no.

1. Check that the data are in place:

r list.files("data") # count_gene.txt, kallisto/, KEGG.gmt, … list.files("data/kallisto") # 8 folders, SRR6068402 … SRR6068409

1. Watch videos F1–F8 and T1–T3 (about 35 minutes in total).

Optional, for module 1, part A only: install kallisto (for example conda install -c bioconda kallisto). This runs on Linux, macOS, or Windows via WSL. The rest of the workshop does not need it, because the kallisto output for all eight samples is provided.