Code review for publication standards

Title: Pin dependency versions: pydeseq2 and torch/torchvision

What
Two direct dependencies are installed without pinned versions, breaking reproducibility of the environment.

Where
Dockerfile:

RUN pip install --no-cache-dir "numpy<2" "pydeseq2" # pydeseq2 unpinned
postInstall:

pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cpu # torch/torchvision unpinned
What to do
Pin pydeseq2== in the Dockerfile and torch== torchvision== in postInstall, using the versions currently resolved.

How to find the current versions

pip freeze | grep -Ei 'pydeseq2|^torch'

What
The README citation block is a placeholder (@article{xxxx}), and the README also has no GitHub repo link (S1 and S2 have one).

Where
README.md — Citation section (and add a repo link near the top).

What to do (when available)
Add the manuscript/preprint link, complete the BibTeX, and add the GitHub repository link.