SpatialQuery 0.0.1__tar.gz

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  1. spatialquery-0.0.1/LICENSE +21 -0
  2. spatialquery-0.0.1/MANIFEST.in +3 -0
  3. spatialquery-0.0.1/PKG-INFO +56 -0
  4. spatialquery-0.0.1/README.md +24 -0
  5. spatialquery-0.0.1/SpatialQuery/__init__.py +3 -0
  6. spatialquery-0.0.1/SpatialQuery/spatial_query.py +1339 -0
  7. spatialquery-0.0.1/SpatialQuery/spatial_query_multiple_fov.py +1116 -0
  8. spatialquery-0.0.1/SpatialQuery/utils.py +130 -0
  9. spatialquery-0.0.1/SpatialQuery.egg-info/PKG-INFO +56 -0
  10. spatialquery-0.0.1/SpatialQuery.egg-info/SOURCES.txt +13 -0
  11. spatialquery-0.0.1/SpatialQuery.egg-info/dependency_links.txt +1 -0
  12. spatialquery-0.0.1/SpatialQuery.egg-info/requires.txt +8 -0
  13. spatialquery-0.0.1/SpatialQuery.egg-info/top_level.txt +1 -0
  14. spatialquery-0.0.1/setup.cfg +4 -0
  15. spatialquery-0.0.1/setup.py +31 -0
spatialquery-0.0.1/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2024 Shaokun An
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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.
spatialquery-0.0.1/MANIFEST.in ADDED
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+ include README.md
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+ include LICENSE
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+
spatialquery-0.0.1/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: SpatialQuery
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+ Version: 0.0.1
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+ Home-page: https://github.com/ShaokunAn/Spatial-Query
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+ Author: Shaokun An
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+ Author-email: shan12@bwh.harvard.edu
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+ License: MIT
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+ Classifier: Development Status :: 3 - Alpha
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+ Classifier: Intended Audience :: Developers
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+ Classifier: Programming Language :: Python :: 3
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+ Requires-Python: >=3.8
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ Requires-Dist: setuptools>=68.0.0
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+ Requires-Dist: anndata>=0.8.0
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+ Requires-Dist: pandas>=2.0.3
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+ Requires-Dist: scipy
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+ Requires-Dist: matplotlib>=3.7.5
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+ Requires-Dist: mlxtend>=0.23.1
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+ Requires-Dist: seaborn>=0.13.2
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+ Requires-Dist: scikit-learn>=1.3.2
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+ Dynamic: author
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+ Dynamic: author-email
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+ Dynamic: classifier
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+ Dynamic: description
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+ Dynamic: description-content-type
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+ Dynamic: home-page
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+ Dynamic: license
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+ Dynamic: license-file
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+ Dynamic: requires-dist
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+ Dynamic: requires-python
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+
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+ SpatialQuery is a package for fast query of Spatial Transcriptomics data.
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+
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+ ### Analysis of ST data in SpatialQuery
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+
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+ With annotated ST data as input, SpatialQuery first builds a k-D tree based on spatial location in each FOV for fast query of neighboring cell compositions. It is composed of methods for single-FOV and multiple-FOVs.
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+ In single-FOV, it contains methods:
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+
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+ - identify frequent patterns across FOV
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+ - identify frequent patterns around cell type of interest
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+ - identify statistically significant patterns around cell type of interest
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+
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+ For multiple-FOVs data, it contains methods:
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+
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+ - identify frequent patterns around cell type of interest in specified datasets
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+ - identify statistically significant patterns around cell type of interest in specified datasets
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+ - identify differential patterns across datasets
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+
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+ ### Installation
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+
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+ ```
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+ pip install -i https://test.pypi.org/simple/ SpatialQuery
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+ ```
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+
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+ For more details, please refer to `examples/SpatialQuery-example.ipynb`.
spatialquery-0.0.1/README.md ADDED
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+ SpatialQuery is a package for fast query of Spatial Transcriptomics data.
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+
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+ ### Analysis of ST data in SpatialQuery
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+
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+ With annotated ST data as input, SpatialQuery first builds a k-D tree based on spatial location in each FOV for fast query of neighboring cell compositions. It is composed of methods for single-FOV and multiple-FOVs.
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+ In single-FOV, it contains methods:
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+
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+ - identify frequent patterns across FOV
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+ - identify frequent patterns around cell type of interest
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+ - identify statistically significant patterns around cell type of interest
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+
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+ For multiple-FOVs data, it contains methods:
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+
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+ - identify frequent patterns around cell type of interest in specified datasets
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+ - identify statistically significant patterns around cell type of interest in specified datasets
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+ - identify differential patterns across datasets
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+
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+ ### Installation
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+
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+ ```
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+ pip install -i https://test.pypi.org/simple/ SpatialQuery
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+ ```
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+
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+ For more details, please refer to `examples/SpatialQuery-example.ipynb`.
spatialquery-0.0.1/SpatialQuery/__init__.py ADDED
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+ from .spatial_query import spatial_query
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+ from .spatial_query_multiple_fov import spatial_query_multi
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+ from .utils import maximal_patterns, retrieve_niche_pattern_freq, plot_niche_pattern_freq