Ecosyste.ms: Issues
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GitHub / vitessce/vitessce-python issues and pull requests
#363 - Fix binder example
Pull Request -
State: closed - Opened by keller-mark 20 days ago
#362 - Enable `numpy` v2 Support/Unpin `numpy` v1
Issue -
State: open - Opened by NickAkhmetov 22 days ago
#361 - Support for H5AD-based AnnData in AnnDataWrapper
Pull Request -
State: closed - Opened by keller-mark 24 days ago
#360 - Misc: Spatial-query, kerchunk, and OME helper functions
Pull Request -
State: closed - Opened by keller-mark about 1 month ago
#359 - Command functions should be able to return an updated config
Issue -
State: open - Opened by keller-mark about 1 month ago
- 1 comment
Labels: feature
#358 - Vitessce python on remote jupyter servers do not work
Issue -
State: closed - Opened by edwin5588 about 1 month ago
- 3 comments
#357 - Unit test for to_dict output following .add_object(AnnDataWrapper(...))
Pull Request -
State: closed - Opened by keller-mark about 2 months ago
#356 - Warn if AnnDataWrapper options are empty as it would result in empty list for `vc['datasets']['files']`
Issue -
State: open - Opened by falexwolf about 2 months ago
- 4 comments
#355 - page_mode and page_esm params
Pull Request -
State: open - Opened by keller-mark about 2 months ago
#354 - Plugin for SpatialQuery
Pull Request -
State: closed - Opened by keller-mark 2 months ago
#353 - Update fill_template.py
Pull Request -
State: closed - Opened by keller-mark 2 months ago
#352 - NickAkhmetov/Copy `requestInit` when using `from_dict`
Pull Request -
State: closed - Opened by NickAkhmetov 2 months ago
#351 - Ability to use comparative views + pageMode in a Jupyter notebook
Issue -
State: open - Opened by keller-mark 3 months ago
Labels: feature, cell-atlas
#350 - Plugin class
Pull Request -
State: closed - Opened by keller-mark 3 months ago
#349 - NickAkhmetov/Cap `numpy` under v2
Pull Request -
State: closed - Opened by NickAkhmetov 4 months ago
- 1 comment
#348 - Support writing plugin_esm using local file with anywidget FileContents
Issue -
State: open - Opened by keller-mark 5 months ago
Labels: feature
#347 - Define a plugin class/dataclass to couple on_config_change and anywidget.invoke handlers with plugin_esm
Issue -
State: closed - Opened by keller-mark 5 months ago
- 1 comment
Labels: feature, cell-atlas
#345 - Adding Vitessce widgets to a visualization dashboard
Issue -
State: closed - Opened by georgezakinih 5 months ago
- 1 comment
#344 - Notebooks errors (list)
Issue -
State: open - Opened by thomcsmits 5 months ago
Labels: bug, docs
#343 - Notebooks environment.yml PackageNotFoundError for starlette==0.14.0
Issue -
State: open - Opened by thomcsmits 5 months ago
Labels: bug
#342 - (chore): supported python versions
Pull Request -
State: closed - Opened by ilan-gold 5 months ago
- 1 comment
#341 - (chore): Clean up `AnnDataWrapper` API
Pull Request -
State: open - Opened by ilan-gold 5 months ago
- 2 comments
#340 - Helper function to use adata.uns[obs_set_col + "_colors"] for initial obs set colors
Issue -
State: open - Opened by keller-mark 5 months ago
Labels: feature
#339 - Setting colors for obsSets?
Issue -
State: open - Opened by srivarra 5 months ago
- 2 comments
#337 - Create module for plugin JS
Pull Request -
State: closed - Opened by keller-mark 6 months ago
#336 - Release v3.2.5
Pull Request -
State: closed - Opened by NickAkhmetov 6 months ago
#335 - NickAkhmetov/Add `requestInit` param to `MultivecZarrWrapper`
Pull Request -
State: closed - Opened by NickAkhmetov 6 months ago
#334 - Support using JSX for writing plugin views
Issue -
State: closed - Opened by keller-mark 6 months ago
Labels: feature
#333 - (feat): `SpatialData` wrapper
Pull Request -
State: open - Opened by ilan-gold 6 months ago
- 9 comments
#332 - Bump version
Pull Request -
State: closed - Opened by keller-mark 6 months ago
- 1 comment
#331 - Support automatic instantiation of Wrapper objects
Issue -
State: open - Opened by keller-mark 6 months ago
- 2 comments
Labels: feature
#330 - pre-commits
Pull Request -
State: open - Opened by giovp 6 months ago
- 1 comment
#329 - Use anywidget-based IPC for zarr gets which do not require serving data on localhost
Pull Request -
State: closed - Opened by keller-mark 6 months ago
- 1 comment
#328 - Versions of anndata, anywidget, JS package
Pull Request -
State: closed - Opened by keller-mark 7 months ago
#327 - Bumping supported Anndata Version?
Issue -
State: closed - Opened by srivarra 7 months ago
- 1 comment
#326 - Update adata_to_multivec
Pull Request -
State: closed - Opened by keller-mark 7 months ago
#325 - Support scope_prefix parameter in link_views_by_dict
Pull Request -
State: closed - Opened by keller-mark 7 months ago
#324 - Support for plugins
Pull Request -
State: closed - Opened by keller-mark 7 months ago
#323 - Proof of concept for spatial-query plugin view
Pull Request -
State: closed - Opened by keller-mark 7 months ago
#322 - Add option for widget to communicate directly with Zarr store (no local HTTP server)
Issue -
State: open - Opened by keller-mark 7 months ago
- 2 comments
Labels: feature
#321 - >1 million cell datasets for demos
Pull Request -
State: open - Opened by keller-mark 8 months ago
- 1 comment
#320 - Additional improvements to adata_to_multivec_zarr function
Issue -
State: open - Opened by keller-mark 8 months ago
Labels: feature
#319 - Split interval conversion logic from the rest of multivec
Pull Request -
State: open - Opened by NickAkhmetov 8 months ago
#318 - ValueError: data too large for non-BigTIFF file
Issue -
State: open - Opened by J-Yash 8 months ago
- 4 comments
#317 - bump js 3.3.3
Pull Request -
State: closed - Opened by keller-mark 8 months ago
#316 - Release
Pull Request -
State: closed - Opened by keller-mark 8 months ago
#315 - Upgrade ome-zarr package
Pull Request -
State: closed - Opened by keller-mark 8 months ago
#314 - Keller mark/mini dataset
Pull Request -
State: open - Opened by keller-mark 8 months ago
#313 - Support additional parameters for imaging wrapper classes to support …
Pull Request -
State: closed - Opened by keller-mark 8 months ago
#312 - Support obsSpots and obsPoints
Pull Request -
State: closed - Opened by keller-mark 8 months ago
#311 - Adding scale bar to spatial view image
Issue -
State: open - Opened by J-Yash 9 months ago
#310 - Minimal example for obsSegmentations.json for visualizing polygons in Spatial View
Issue -
State: open - Opened by J-Yash 9 months ago
- 2 comments
#309 - OmeTiffWrapper - support coordinationValues and fileType: "image.ome-tiff"
Issue -
State: closed - Opened by keller-mark 9 months ago
#308 - AnnDataWrapper - support for obsSpots, obsPoints, etc.
Issue -
State: closed - Opened by keller-mark 9 months ago
#307 - Example using 10x Space Ranger outputs
Pull Request -
State: open - Opened by keller-mark 11 months ago
#306 - Publish a Vitessce notebook on Posit Connect
Issue -
State: closed - Opened by georgezakinih 11 months ago
- 11 comments
#305 - Failed to load model class "Anymodel"
Issue -
State: closed - Opened by CReihsmann 11 months ago
- 2 comments
#304 - Matt scott68/unzip
Pull Request -
State: open - Opened by mattscott68 12 months ago
#303 - Use v3.3.0
Pull Request -
State: closed - Opened by keller-mark about 1 year ago
#302 - Fix use_coordination function
Pull Request -
State: closed - Opened by keller-mark about 1 year ago
#301 - Version bump
Pull Request -
State: closed - Opened by keller-mark about 1 year ago
#300 - Bump js package version
Pull Request -
State: closed - Opened by keller-mark about 1 year ago
#299 - Add file extensions
Pull Request -
State: closed - Opened by keller-mark about 1 year ago
#298 - Convert spatialdata-plot plotting tree to Vitessce config
Issue -
State: open - Opened by keller-mark about 1 year ago
Labels: feature
#297 - Demos for SquidPy example datasets
Issue -
State: open - Opened by keller-mark about 1 year ago
Labels: data_utils, demo
#296 - Snakemake pipeline for 10x Genomics Multiome outputs
Issue -
State: open - Opened by keller-mark about 1 year ago
Labels: data_utils
#295 - Bump version
Pull Request -
State: closed - Opened by keller-mark about 1 year ago
#294 - Convert flattened multi-level coordination JSON back to nested dict for `to_python`
Issue -
State: open - Opened by keller-mark about 1 year ago
Labels: feature, cell-atlas
#293 - Support emObject
Issue -
State: open - Opened by keller-mark over 1 year ago
Labels: data_utils
#292 - Support RDS files
Issue -
State: open - Opened by keller-mark over 1 year ago
Labels: data_utils
#291 - Support Spatial CUT&tag and spatial ATAC formats
Issue -
State: open - Opened by keller-mark over 1 year ago
Labels: data_utils
#290 - Support Vizgen example formats
Issue -
State: open - Opened by keller-mark over 1 year ago
Labels: data_utils
#289 - Support Nanostring example formats
Issue -
State: open - Opened by keller-mark over 1 year ago
Labels: data_utils
#288 - Support cellranger outputs
Issue -
State: open - Opened by keller-mark over 1 year ago
Labels: data_utils
#287 - Support SpatialTis
Issue -
State: open - Opened by keller-mark over 1 year ago
Labels: data_utils
#286 - Support SpatialData
Issue -
State: open - Opened by keller-mark over 1 year ago
- 3 comments
Labels: data_utils
#285 - Support spateo formats
Issue -
State: open - Opened by keller-mark over 1 year ago
Labels: data_utils
#284 - Support MuData objects
Issue -
State: open - Opened by keller-mark over 1 year ago
- 1 comment
Labels: data_utils
#283 - Support bento formats
Issue -
State: open - Opened by keller-mark over 1 year ago
Labels: data_utils
#282 - Support writing pyramidal OME-TIFF and OME-NGFF
Issue -
State: open - Opened by keller-mark over 1 year ago
Labels: data_utils
#281 - Support 10X genomics HDF5 files
Issue -
State: open - Opened by keller-mark over 3 years ago
Labels: data_utils
#280 - Support Seurat data objects
Issue -
State: open - Opened by keller-mark over 3 years ago
Labels: data_utils
#279 - Support Starfish data objects
Issue -
State: open - Opened by keller-mark over 3 years ago
- 4 comments
Labels: data_utils
#278 - Support BiocPy SingleCellExperiment
Issue -
State: open - Opened by keller-mark about 1 year ago
Labels: data_utils
#277 - Refactor data_utils
Pull Request -
State: open - Opened by keller-mark about 1 year ago
#276 - Refactor data_utils and extras_require
Issue -
State: open - Opened by keller-mark about 1 year ago
- 1 comment
Labels: data_utils
#275 - Release 3.0.7
Pull Request -
State: closed - Opened by NickAkhmetov about 1 year ago
#274 - NickAkhmetov/Add `allow_multiple_scopes_per_type` boolean arg to `use_coordination` and `link_views`
Pull Request -
State: closed - Opened by NickAkhmetov about 1 year ago
#273 - NickAkhmetov/Update `CoordinationType` and `FileType` to match docs
Pull Request -
State: closed - Opened by NickAkhmetov about 1 year ago
#272 - NickAkhmetov/Add support for `obs_labels_names` and `obs_labels_paths` arrays
Pull Request -
State: closed - Opened by NickAkhmetov about 1 year ago
- 1 comment
#271 - ViewConfig.`use_coordination` with multiple coordinations of same type
Issue -
State: closed - Opened by NickAkhmetov about 1 year ago
#270 - Update `FileType` enum to match JS API values
Issue -
State: closed - Opened by NickAkhmetov about 1 year ago
- 1 comment
#269 - Support `uid` field in VitessceConfig constructor
Issue -
State: open - Opened by keller-mark about 1 year ago
Labels: feature, cell-atlas
#268 - Release
Pull Request -
State: closed - Opened by keller-mark about 1 year ago
#267 - Upgrade dynamic-import package version to fix bug
Pull Request -
State: closed - Opened by keller-mark about 1 year ago
#266 - Complex coordination port
Pull Request -
State: closed - Opened by keller-mark about 1 year ago
#265 - Revert removal of data_type argument for VitessceConfigDatasetFile
Issue -
State: open - Opened by keller-mark about 1 year ago
Labels: enhancement
#264 - Keller mark/issue 1228 pr
Pull Request -
State: closed - Opened by keller-mark about 1 year ago
#263 - Create a script that converts CellBrowser config to Anndata-Zarr file which is digestable by Vitessce zero config mode
Pull Request -
State: closed - Opened by ivababukova about 1 year ago
#262 - Revert "Create a script that converts CellBrowser config to Anndata-Zarr file which is digestable by Vitessce zero config mode"
Pull Request -
State: closed - Opened by ivababukova about 1 year ago