@vitessce/all 2.0.0-beta.0

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Files changed (5) hide show
  1. package/LICENSE +21 -0
  2. package/README.md +1 -0
  3. package/dist/index.js +1 -0
  4. package/dist/setup.js +96 -0
  5. package/package.json +44 -0
package/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2018
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
package/README.md ADDED
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+ This package exports a `<Vitessce/>` component with all available plugins and file types registered.
package/dist/index.js ADDED
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+ export { Vitessce } from './setup';
package/dist/setup.js ADDED
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+ import { jsx as _jsx } from "react/jsx-runtime";
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+ /* eslint-disable max-len */
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+ import { useState, useLayoutEffect } from 'react';
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+ import { VitS, registerPluginFileType } from '@vitessce/vit-s';
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+ // Register view type plugins
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+ import { register as registerDescription } from '@vitessce/description';
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+ import { register as registerObsSetsManager } from '@vitessce/obs-sets-manager';
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+ import { register as registerScatterplotEmbedding } from '@vitessce/scatterplot-embedding';
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+ import { register as registerScatterplotGating } from '@vitessce/scatterplot-gating';
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+ import { register as registerSpatial } from '@vitessce/spatial';
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+ import { register as registerHeatmap } from '@vitessce/heatmap';
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+ import { register as registerFeatureList } from '@vitessce/feature-list';
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+ import { register as registerLayerController } from '@vitessce/layer-controller';
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+ import { register as registerStatus } from '@vitessce/status';
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+ import { registerCellSetExpression, registerCellSetSizes, registerExpressionHistogram } from '@vitessce/statistical-plots';
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+ import { registerHiglass, registerGenomicProfiles } from '@vitessce/genomic-profiles';
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+ // Register file type plugins
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+ import {
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+ // CSV
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+ CsvSource, ObsSetsCsvLoader, ObsEmbeddingCsvLoader, ObsLocationsCsvLoader, ObsLabelsCsvLoader, ObsFeatureMatrixCsvLoader, FeatureLabelsCsvLoader, } from '@vitessce/csv';
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+ import {
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+ // JSON
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+ JsonSource, JsonLoader, ObsSegmentationsJsonLoader, ObsSetsJsonLoader,
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+ // Legacy
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+ RasterJsonAsImageLoader, RasterJsonAsObsSegmentationsLoader, ClustersJsonAsObsFeatureMatrixLoader, GenesJsonAsObsFeatureMatrixLoader, CellsJsonAsObsLabelsLoader, CellsJsonAsObsEmbeddingLoader, CellsJsonAsObsLocationsLoader, CellsJsonAsObsSegmentationsLoader, MoleculesJsonAsObsLocationsLoader, MoleculesJsonAsObsLabelsLoader, } from '@vitessce/json';
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+ import {
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+ // AnnData
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+ AnnDataSource, ObsFeatureMatrixAnndataLoader, ObsEmbeddingAnndataLoader, ObsLocationsAnndataLoader, ObsSegmentationsAnndataLoader, ObsSetsAnndataLoader, ObsLabelsAnndataLoader, FeatureLabelsAnndataLoader,
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+ // OME
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+ OmeZarrLoader,
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+ // Legacy
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+ ZarrDataSource, MatrixZarrAsObsFeatureMatrixLoader, GenomicProfilesZarrLoader, } from '@vitessce/zarr';
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+ import { FileType, DataType } from '@vitessce/constants-internal';
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+ function setup() {
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+ // View types
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+ registerDescription();
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+ registerObsSetsManager();
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+ registerScatterplotEmbedding();
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+ registerScatterplotGating();
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+ registerSpatial();
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+ registerHeatmap();
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+ registerFeatureList();
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+ registerLayerController();
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+ registerStatus();
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+ // Statistical plots
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+ registerCellSetExpression();
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+ registerCellSetSizes();
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+ registerExpressionHistogram();
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+ // Higlass
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+ registerHiglass();
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+ registerGenomicProfiles();
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+ // File types
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+ // All CSV file types
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+ registerPluginFileType(FileType.OBS_SETS_CSV, DataType.OBS_SETS, ObsSetsCsvLoader, CsvSource);
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+ registerPluginFileType(FileType.OBS_EMBEDDING_CSV, DataType.OBS_EMBEDDING, ObsEmbeddingCsvLoader, CsvSource);
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+ registerPluginFileType(FileType.OBS_LOCATIONS_CSV, DataType.OBS_LOCATIONS, ObsLocationsCsvLoader, CsvSource);
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+ registerPluginFileType(FileType.OBS_LABELS_CSV, DataType.OBS_LABELS, ObsLabelsCsvLoader, CsvSource);
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+ registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CSV, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixCsvLoader, CsvSource);
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+ registerPluginFileType(FileType.FEATURE_LABELS_CSV, DataType.FEATURE_LABELS, FeatureLabelsCsvLoader, CsvSource);
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+ // All JSON file types
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+ registerPluginFileType(FileType.OBS_SEGMENTATIONS_JSON, DataType.OBS_SEGMENTATIONS, ObsSegmentationsJsonLoader, JsonSource);
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+ registerPluginFileType(FileType.OBS_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
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+ // All AnnData file types
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+ registerPluginFileType(FileType.OBS_SETS_ANNDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, AnnDataSource);
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+ registerPluginFileType(FileType.OBS_EMBEDDING_ANNDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, AnnDataSource);
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+ registerPluginFileType(FileType.OBS_LOCATIONS_ANNDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, AnnDataSource);
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+ registerPluginFileType(FileType.OBS_LABELS_ANNDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, AnnDataSource);
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+ registerPluginFileType(FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, AnnDataSource);
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+ registerPluginFileType(FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource);
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+ registerPluginFileType(FileType.FEATURE_LABELS_ANNDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource);
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+ // All OME file types
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+ registerPluginFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource);
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+ // All legacy file types
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+ registerPluginFileType(FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR, DataType.OBS_FEATURE_MATRIX, MatrixZarrAsObsFeatureMatrixLoader, ZarrDataSource);
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+ registerPluginFileType(FileType.IMAGE_RASTER_JSON, DataType.IMAGE, RasterJsonAsImageLoader, JsonSource);
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+ registerPluginFileType(FileType.OBS_SEGMENTATIONS_RASTER_JSON, DataType.OBS_SEGMENTATIONS, RasterJsonAsObsSegmentationsLoader, JsonSource);
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+ registerPluginFileType(FileType.OBS_SETS_CELL_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
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+ registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON, DataType.OBS_FEATURE_MATRIX, ClustersJsonAsObsFeatureMatrixLoader, JsonSource);
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+ registerPluginFileType(FileType.OBS_FEATURE_MATRIX_GENES_JSON, DataType.OBS_FEATURE_MATRIX, GenesJsonAsObsFeatureMatrixLoader, JsonSource);
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+ registerPluginFileType(FileType.OBS_LABELS_CELLS_JSON, DataType.OBS_LABELS, CellsJsonAsObsLabelsLoader, JsonSource);
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+ registerPluginFileType(FileType.OBS_EMBEDDING_CELLS_JSON, DataType.OBS_EMBEDDING, CellsJsonAsObsEmbeddingLoader, JsonSource);
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+ registerPluginFileType(FileType.OBS_LOCATIONS_CELLS_JSON, DataType.OBS_LOCATIONS, CellsJsonAsObsLocationsLoader, JsonSource);
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+ registerPluginFileType(FileType.OBS_SEGMENTATIONS_CELLS_JSON, DataType.OBS_SEGMENTATIONS, CellsJsonAsObsSegmentationsLoader, JsonSource);
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+ registerPluginFileType(FileType.OBS_LOCATIONS_MOLECULES_JSON, DataType.OBS_LOCATIONS, MoleculesJsonAsObsLocationsLoader, JsonSource);
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+ registerPluginFileType(FileType.OBS_LABELS_MOLECULES_JSON, DataType.OBS_LABELS, MoleculesJsonAsObsLabelsLoader, JsonSource);
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+ registerPluginFileType(FileType.NEIGHBORHOODS_JSON, DataType.NEIGHBORHOODS, JsonLoader, JsonSource);
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+ registerPluginFileType(FileType.GENOMIC_PROFILES_ZARR, DataType.GENOMIC_PROFILES, GenomicProfilesZarrLoader, ZarrDataSource);
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+ }
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+ export function Vitessce(props) {
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+ const [ready, setReady] = useState(false);
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+ useLayoutEffect(() => {
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+ setup();
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+ setReady(true);
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+ }, []);
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+ return (ready ? (_jsx(VitS, { ...props })) : null);
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+ }
package/package.json ADDED
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+ {
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+ "name": "@vitessce/all",
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+ "version": "2.0.0-beta.0",
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+ "author": "Gehlenborg Lab",
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+ "homepage": "http://vitessce.io",
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+ "repository": {
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+ "type": "git",
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+ "url": "git+https://github.com/vitessce/vitessce.git"
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+ },
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+ "license": "MIT",
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+ "main": "dist/index.js",
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+ "files": [
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+ "dist"
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+ ],
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+ "dependencies": {
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+ "@material-ui/core": "~4.12.3",
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+ "@vitessce/constants-internal": "2.0.0-beta.0",
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+ "@vitessce/csv": "2.0.0-beta.0",
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+ "@vitessce/description": "2.0.0-beta.0",
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+ "@vitessce/feature-list": "2.0.0-beta.0",
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+ "@vitessce/genomic-profiles": "2.0.0-beta.0",
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+ "@vitessce/heatmap": "2.0.0-beta.0",
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+ "@vitessce/json": "2.0.0-beta.0",
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+ "@vitessce/layer-controller": "2.0.0-beta.0",
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+ "@vitessce/obs-sets-manager": "2.0.0-beta.0",
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+ "@vitessce/scatterplot-embedding": "2.0.0-beta.0",
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+ "@vitessce/scatterplot-gating": "2.0.0-beta.0",
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+ "@vitessce/spatial": "2.0.0-beta.0",
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+ "@vitessce/statistical-plots": "2.0.0-beta.0",
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+ "@vitessce/status": "2.0.0-beta.0",
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+ "@vitessce/vit-s": "2.0.0-beta.0",
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+ "@vitessce/zarr": "2.0.0-beta.0"
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+ },
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+ "devDependencies": {
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+ "react": "^18.0.0"
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+ },
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+ "peerDependencies": {
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+ "react": "^16.8.0 || ^17.0.0 || ^18.0.0"
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+ },
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+ "scripts": {
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+ "start": "tsc --watch",
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+ "build": "tsc"
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+ }
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+ }