Comments (1)
keller-mark
commented on July 2, 2024
1
The top-level environment is for the development of the vitessce package itself.
The inner environment is for running the example notebooks in docs/notebooks. The package does not depend on Jupyter or ScanPy, for instance, but running the notebooks does.
We do have a second readme at docs/notebooks/README.md but you have a good point that we should explain this in the root README.md.
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Related Issues (20)
- Refactor data_utils and extras_require HOT 1
- Support BiocPy SingleCellExperiment
- Convert flattened multi-level coordination JSON back to nested dict for `to_python`
- Snakemake pipeline for 10x Genomics Multiome outputs
- Demos for SquidPy example datasets
- Convert spatialdata-plot plotting tree to Vitessce config
- Failed to load model class "Anymodel" HOT 2
- Publish a Vitessce notebook on Posit Connect HOT 11
- AnnDataWrapper - support for obsSpots, obsPoints, etc.
- OmeTiffWrapper - support coordinationValues and fileType: "image.ome-tiff"
- Minimal example for obsSegmentations.json for visualizing polygons in Spatial View HOT 2
- Adding scale bar to spatial view image
- ValueError: data too large for non-BigTIFF file HOT 4
- Additional improvements to adata_to_multivec_zarr function
- Add option for widget to communicate directly with Zarr store (no local HTTP server) HOT 2
- Bumping supported Anndata Version? HOT 1
- Support automatic instantiation of Wrapper objects HOT 2
- Support using JSX for writing plugin views
- Setting colors for obsSets? HOT 2
- Helper function to use adata.uns[obs_set_col + "_colors"] for initial obs set colors
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