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LIF Workshop Exercises

Live-coding exercises for a GTEx-based LIF cachexia correlation analysis. This branch contains everything needed to run the workshop independently — no other files from the main repository are required.

Contents

Path Description
exercises-live-coding/ Workshop exercise notebooks and setup scripts
workshopr/ Local R helper package required by the exercises
scripts/gtex-metadata-fetch.R Step 1: fetch GTEx sample metadata from the API
scripts/gtex-expression-qc.R Step 2: download and QC expression data; writes the cache
usr-inputs/ Workshop preferences file and gene input template

Setup

Open R and install dependencies:

install.packages(c(
  "dplyr", "tidyr", "tibble", "readr", "stringr", "cli",
  "msigdbr", "matrixStats", "pheatmap", "RColorBrewer", "ggplot2"
))

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("fgsea")

devtools::install("workshopr")

Generate the data cache

Run these two scripts in order from the repo root. Data is written to data/gtex/ (gitignored).

source("scripts/gtex-metadata-fetch.R")
source("scripts/gtex-expression-qc.R")

This will take several minutes on first run. The output file data/gtex/expression-qc/expression_qc_cache.rds is required by the main exercise.

Run the exercises

File Description
exercises-live-coding/00-live-setup.R Environment check — run first to confirm everything is installed
exercises-live-coding/01-live-expression-prep.R Walkthrough of the expression QC pipeline
exercises-live-coding/02-lif-correlation-analysis-live.qmd Main exercise: LIF co-expression → GSEA → hypothesis

Open 02-lif-correlation-analysis-live.qmd in RStudio and run chunks interactively, or render:

quarto::quarto_render("exercises-live-coding/02-lif-correlation-analysis-live.qmd")

Reference

The full annotated analysis (including MF/CC GO terms, dot plots, and clinical translation questions) is in the main repository under docs/gtex-vignettes/gtex-expression-lif-analysis.qmd.