Name		Name	Last commit message	Last commit date
parent directory ..
.envrc		.envrc
README.md		README.md
cellbrowser_to_vitessce_config_conversion.ipynb		cellbrowser_to_vitessce_config_conversion.ipynb
config_to_python.ipynb		config_to_python.ipynb
data_conversion.ipynb		data_conversion.ipynb
data_export_files.ipynb		data_export_files.ipynb
data_export_s3.ipynb		data_export_s3.ipynb
environment.yml		environment.yml
example_configs.py		example_configs.py
web_app_brain.ipynb		web_app_brain.ipynb
widget_brain.ipynb		widget_brain.ipynb
widget_brain_with_base_dir.ipynb		widget_brain_with_base_dir.ipynb
widget_from_dict.ipynb		widget_from_dict.ipynb
widget_genomic_profiles.ipynb		widget_genomic_profiles.ipynb
widget_imaging.ipynb		widget_imaging.ipynb
widget_imaging_beta.ipynb		widget_imaging_beta.ipynb
widget_imaging_segmentation.ipynb		widget_imaging_segmentation.ipynb
widget_loom.ipynb		widget_loom.ipynb
widget_on_colab.ipynb		widget_on_colab.ipynb
widget_pbmc.ipynb		widget_pbmc.ipynb
widget_pbmc_remote.ipynb		widget_pbmc_remote.ipynb
widget_shortcut.ipynb		widget_shortcut.ipynb

README.md

Example Notebooks

The notebooks contained in this directory demonstrate the Vitessce Python package functionality.

Setup

Some of the example notebooks rely on external single-cell data analysis packages. An environment containing these additional packages can be installed with conda or pip.

cd docs/notebooks
conda env create -f environment.yml
conda activate vitessce-python-notebooks
pip install -e "../..[dev]"

Run

jupyter lab

Troubleshooting

If you previously had the vitessce Python package v1 installed, you may need to uninstall the previous lab extension due to conflicts between the v1 and v2 widget JS code.

jupyter labextension uninstall vitessce-jupyter

Files

notebooks

Directory actions

More options

Directory actions

More options

Latest commit

History

notebooks

Folders and files

parent directory

Example Notebooks

Setup

Run

Troubleshooting