F2-study-app

Interactive Shiny application to the study A novel mouse cross uncovers candidate therapeutic targets for hepatic steatosis, adiposity, and dyslipidemia.

Explore the study's data from the F2 mouse cross: metabolic phenotypes, liver RNA-seq and proteomics, and QTL/LOD genetic mapping through interactive plots and tables.

Live app: https://lisp-lms.shinyapps.io/F2_study/

Running the app locally

To run it from this repository, you must download the F2_processed_data.tar.gz (~180 MB) from the latest release and extract it in the repository root:

curl -L -o F2_processed_data.tar.gz \
  https://github.com/auwerxlab/F2-study-app/releases/download/v1.0/F2_processed_data.tar.gz
tar -xzf F2_processed_data.tar.gz

This creates the Data/ folder the app reads at startup. Then install the pinned R dependencies and launch the app:

install.packages("renv")
source("renv/activate.R")
renv::restore()   # install the exact package versions from renv.lock (first run only)
shiny::runApp()

Raw / source data (optional, to change parameters). The processed bundles above are precomputed with the study's default settings. To recompute them with different parameters, download the raw source data from Zenodo:

DOI: 10.5281/zenodo.21336282

Place the files under Data/ (extract qtl_scans.zip there), then re-run the relevant Scripts/preprocess_*.R scripts, which write updated bundles back into Data/. Each raw file and how it was produced is documented in the Zenodo record's README.

• For questions related to the
  • study, please contact Giorgia Benegiamo: Giorgia.Benegiamo@epfl.ch
  • app, please contact Alaa Badreddine: Alaa.Badreddine@epfl.ch