NF1_organoid_profile_analysis

This repo contains analysis code of profiles generated in multiple image-based profiling repos.

• 3D image-based profiles of NF1 organoids were generated from: NF1 3D Organoid profiling pipeline
• 2D image-based profiles of NF1 organoids were generated from: NF1 2D organoid profiling pipeline
• Cell types will be predicted using: Cell type prediction in NF1 organoids

Repo modules

• 0.download_data: Download image-based profiles from the internet (not yet available)
• 1.EDA: Exploratory data analysis of image-based profiles

Computational environment

Notebooks in this repo are split between Python and R, each managed by a separate environment.

Python (uv)

Python notebooks use a uv-managed virtual environment defined in pyproject.toml/uv.lock.

source uv_setup.sh

This creates .venv and registers a python3 Jupyter kernel. Select this kernel when running the Python notebooks.

R (mamba)

R notebooks use a mamba/conda environment defined in environments/r_env.yml.

mamba env create -f environments/r_env.yml
# or, if the environment already exists:
mamba env update -f environments/r_env.yml

This creates the gff_figure_env environment but does not register a Jupyter kernel for it. Register the kernel once, from inside the activated environment:

mamba activate gff_figure_env
Rscript -e 'IRkernel::installspec(name = "gff_figure_env", displayname = "R (gff_figure_env)")'

Select the R (gff_figure_env) kernel when running the R notebooks for visualization.