docker-scri-notebook

Basic Jupyter Notebook environment for single-cell analysis using Python and R.

Base Image

jupyter/datascience-notebook:notebook-6.4.0

Selecting an image: https://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html

Installed Packages

Python v3.9.6

scanpy==1.8.1
anndata==0.7.6
umap==0.5.1
numpy==1.21.1
scipy==1.7.1
pandas==1.3.1
scikit-learn==0.24.2
statsmodels==0.12.2
python-igraph==0.9.6
pynndescent==0.5.4
papermill==2.3.3
rpy2

R v4.1.0

Bioconductor=3.13
BiocManager=1.30.16
SingleCellExperiment=1.14.1

Running Notebook

./run-notebook.sh

Build Container Image

./build.sh

Push to Docker Registry

Either you can use the docker push command or run push.sh (requires SCING):

./push.sh