Robust Data-driven gene expression inference for RNA-seq using curated intergenic regions

This repository contains the notebooks, data, and outputs used to regenerate the figures for the paper:

Robust Data-driven gene expression inference for RNA-seq using curated intergenic regions
Alessandro Brandulas Cammarata, Sara S. Fonseca Costa, Marta Rosikiewicz, Julien Roux, Julien Wollbrett, Frederic B. Bastian, Marc Robinson-Rechavi

Affiliations:

• Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
• SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
• Present address: Bioinformatics Core Facility, Department of Biomedicine, University of Basel, Switzerland

Equal last author and corresponding author: frederic.bastian@sib.swiss; marc.robinson-rechavi@unil.ch

Repository layout

• notebooks/: Jupyter notebooks for each figure.
• data/: Input data used by the notebooks.
• output_files/: Generated tables and intermediate outputs.
• figures/: Rendered figures.
• Dockerfile, requirements.txt, DOCKER.md: Reproducible environment setup.

Data

Data used to generate the figures of the paper can be found in the data/ directory except for the subsampling_results/ data which has to be downloaded from zenodo (https://zenodo.org/records/19347960) due to its large size.

Quick start (Docker)

Build the image from the repo root:

docker build -t bgee-calls .

Launch Jupyter Lab:

docker run --rm -it -p 8888:8888 -v "$PWD":/workspace -w /workspace/notebooks bgee-calls \
  jupyter lab --ip=0.0.0.0 --no-browser --ServerApp.token='' --ServerApp.password=''

Then open http://localhost:8888/lab.

Run all notebooks headlessly (in place):

docker run --rm -it -v "$PWD":/workspace -w /workspace/notebooks bgee-calls \
  bash -lc 'for nb in *.ipynb; do jupyter nbconvert --to notebook --execute --inplace "$nb"; done'

More Docker usage details are in DOCKER.md.

Local (non-Docker) run

Create a Python environment and install dependencies:

python3 -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

Then start Jupyter Lab from notebooks/:

cd notebooks
jupyter lab

Notes

• Notebooks assume relative paths like ../data/... and ../output_files/....
• Outputs and figures are written to the existing output_files/ and figures/ folders.

Citation

If you use this repository, please cite the paper:

Robust Data-driven gene expression inference for RNA-seq using curated intergenic regions
Brandulas Cammarata A., Fonseca Costa S.S., Rosikiewicz M., Roux J., Wollbrett J., Bastian F.B., Robinson-Rechavi M.