scMultiChat 0.1.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (39) hide show
  1. MultiChat/Analysis/Intra_strength.py +1758 -0
  2. MultiChat/Analysis/Processing.py +152 -0
  3. MultiChat/Analysis/__init__.py +2 -0
  4. MultiChat/Heterogeneous_g_emb/__init__.py +13 -0
  5. MultiChat/Heterogeneous_g_emb/_settings.py +156 -0
  6. MultiChat/Heterogeneous_g_emb/_utils.py +143 -0
  7. MultiChat/Heterogeneous_g_emb/_version.py +3 -0
  8. MultiChat/Heterogeneous_g_emb/plotting/__init__.py +19 -0
  9. MultiChat/Heterogeneous_g_emb/plotting/_palettes.py +180 -0
  10. MultiChat/Heterogeneous_g_emb/plotting/_plot.py +1498 -0
  11. MultiChat/Heterogeneous_g_emb/plotting/_post_training.py +742 -0
  12. MultiChat/Heterogeneous_g_emb/plotting/_utils.py +103 -0
  13. MultiChat/Heterogeneous_g_emb/preprocessing/__init__.py +26 -0
  14. MultiChat/Heterogeneous_g_emb/preprocessing/_general.py +91 -0
  15. MultiChat/Heterogeneous_g_emb/preprocessing/_pca.py +182 -0
  16. MultiChat/Heterogeneous_g_emb/preprocessing/_qc.py +727 -0
  17. MultiChat/Heterogeneous_g_emb/preprocessing/_utils.py +60 -0
  18. MultiChat/Heterogeneous_g_emb/preprocessing/_variable_genes.py +82 -0
  19. MultiChat/Heterogeneous_g_emb/readwrite.py +250 -0
  20. MultiChat/Heterogeneous_g_emb/tools/__init__.py +23 -0
  21. MultiChat/Heterogeneous_g_emb/tools/_gene_scores.py +346 -0
  22. MultiChat/Heterogeneous_g_emb/tools/_general.py +71 -0
  23. MultiChat/Heterogeneous_g_emb/tools/_integration.py +197 -0
  24. MultiChat/Heterogeneous_g_emb/tools/_pbg.py +1184 -0
  25. MultiChat/Heterogeneous_g_emb/tools/_post_training.py +919 -0
  26. MultiChat/Heterogeneous_g_emb/tools/_umap.py +58 -0
  27. MultiChat/Heterogeneous_g_emb/tools/_utils.py +253 -0
  28. MultiChat/Model/Layers.py +116 -0
  29. MultiChat/Model/__init__.py +3 -0
  30. MultiChat/Model/model_training.py +166 -0
  31. MultiChat/Model/modules.py +93 -0
  32. MultiChat/Model/utilities.py +234 -0
  33. MultiChat/Plot/Visualization.py +470 -0
  34. MultiChat/Plot/__init__.py +1 -0
  35. MultiChat/__init__.py +12 -0
  36. scmultichat-0.1.0.dist-info/METADATA +156 -0
  37. scmultichat-0.1.0.dist-info/RECORD +39 -0
  38. scmultichat-0.1.0.dist-info/WHEEL +5 -0
  39. scmultichat-0.1.0.dist-info/top_level.txt +1 -0
MultiChat/Plot/__init__.py ADDED
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+ from . import Visualization
MultiChat/__init__.py ADDED
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+ """
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+ MultiChat
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+ # Version: 0.1.0
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+ # Author: Caiwei Zhen
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+ """
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+
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+ from .Model import utilities, model_training
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+ from .Analysis import Processing, Intra_strength
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+ from .Plot import Visualization
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+
11
+ __version__ = "0.1.0"
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+ __author__ = "Caiwei Zhen"
scmultichat-0.1.0.dist-info/METADATA ADDED
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1
+ Metadata-Version: 2.4
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+ Name: scMultiChat
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+ Version: 0.1.0
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+ Summary: Cell-cell communication using MultiChat
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+ Author: Caiwei Zhen
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+ Author-email: cwzhen@whu.edu.cn
7
+ Requires-Python: >=3.12
8
+ Requires-Dist: adbc-driver-manager==1.7.0
9
+ Requires-Dist: adbc-driver-sqlite==1.7.0
10
+ Requires-Dist: adjustText==1.3.0
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+ Requires-Dist: altair==5.5.0
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+ Requires-Dist: anndata==0.12.2
13
+ Requires-Dist: annotated-types==0.7.0
14
+ Requires-Dist: array-api-compat==1.12.0
15
+ Requires-Dist: arro3-core==0.6.1
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+ Requires-Dist: asttokens==3.0.0
17
+ Requires-Dist: attrs==25.3.0
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+ Requires-Dist: babel==2.17.0
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+ Requires-Dist: blosc2==3.7.2
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+ Requires-Dist: cachetools==5.5.2
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+ Requires-Dist: certifi==2025.8.3
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+ Requires-Dist: charset-normalizer==3.4.3
23
+ Requires-Dist: click==8.2.1
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+ Requires-Dist: cloudpickle==3.1.1
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+ Requires-Dist: comm==0.2.3
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+ Requires-Dist: commonmark==0.9.1
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+ Requires-Dist: connectorx==0.4.4
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+ Requires-Dist: contourpy==1.3.3
29
+ Requires-Dist: crc32c==2.7.1
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+ Requires-Dist: cycler==0.12.1
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+ Requires-Dist: debugpy==1.8.16
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+ Requires-Dist: decorator==5.2.1
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+ Requires-Dist: deltalake==1.1.4
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+ Requires-Dist: Deprecated==1.2.18
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+ Requires-Dist: donfig==0.8.1.post1
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+ Requires-Dist: et_xmlfile==2.0.0
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+ Requires-Dist: exceptiongroup==1.3.0
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+ Requires-Dist: executing==2.2.0
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+ Requires-Dist: faicons==0.2.2
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+ Requires-Dist: fastexcel==0.14.0
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+ Requires-Dist: filelock==3.19.1
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+ Requires-Dist: fonttools==4.59.1
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+ Requires-Dist: fsspec==2025.7.0
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+ Requires-Dist: gevent==25.5.1
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+ Requires-Dist: great-tables==0.18.0
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+ Requires-Dist: greenlet==3.2.4
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+ Requires-Dist: h5py==3.14.0
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+ Requires-Dist: htmltools==0.6.0
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+ Requires-Dist: idna==3.10
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+ Requires-Dist: importlib_metadata==8.7.0
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+ Requires-Dist: importlib_resources==6.5.2
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+ Requires-Dist: ipykernel==6.30.1
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+ Requires-Dist: ipython==9.4.0
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+ Requires-Dist: ipython_pygments_lexers==1.1.1
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+ Requires-Dist: jedi==0.19.2
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+ Requires-Dist: Jinja2==3.1.6
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+ Requires-Dist: joblib==1.5.2
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+ Requires-Dist: jsonschema==4.25.1
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+ Requires-Dist: jsonschema-specifications==2025.4.1
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+ Requires-Dist: jupyter_client==8.6.3
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+ Requires-Dist: jupyter_core==5.8.1
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+ Requires-Dist: kiwisolver==1.4.9
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+ Requires-Dist: kneed==0.8.5
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+ Requires-Dist: legacy-api-wrap==1.4.1
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+ Requires-Dist: llvmlite==0.44.0
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+ Requires-Dist: markdown-it-py==4.0.0
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+ Requires-Dist: MarkupSafe==3.0.2
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+ Requires-Dist: matplotlib==3.10.5
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+ Requires-Dist: matplotlib-inline==0.1.7
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+ Requires-Dist: mdurl==0.1.2
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+ Requires-Dist: mmh3==5.2.0
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+ Requires-Dist: mpmath==1.3.0
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+ Requires-Dist: msgpack==1.1.1
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+ Requires-Dist: narwhals==2.2.0
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+ Requires-Dist: natsort==8.4.0
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+ Requires-Dist: ndindex==1.10.0
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+ Requires-Dist: nest_asyncio==1.6.0
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+ Requires-Dist: networkx==3.5
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+ Requires-Dist: numba==0.61.2
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+ Requires-Dist: numcodecs==0.16.2
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+ Requires-Dist: numexpr==2.11.0
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+ Requires-Dist: numpy==2.2.0
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+ Requires-Dist: openpyxl==3.1.5
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+ Requires-Dist: packaging==25.0
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+ Requires-Dist: pandas==2.3.2
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+ Requires-Dist: parso==0.8.5
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+ Requires-Dist: patsy==1.0.1
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+ Requires-Dist: pexpect==4.9.0
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+ Requires-Dist: pickleshare==0.7.5
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+ Requires-Dist: pillow==11.3.0
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+ Requires-Dist: platformdirs==4.4.0
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+ Requires-Dist: plotly==6.3.0
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+ Requires-Dist: polars==1.32.3
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+ Requires-Dist: prompt_toolkit==3.0.51
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+ Requires-Dist: psutil==7.0.0
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+ Requires-Dist: ptyprocess==0.7.0
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+ Requires-Dist: pure_eval==0.2.3
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+ Requires-Dist: py-cpuinfo==9.0.0
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+ Requires-Dist: pyarrow==21.0.0
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+ Requires-Dist: pybedtools==0.12.0
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+ Requires-Dist: pydantic==2.11.7
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+ Requires-Dist: pydantic_core==2.33.2
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+ Requires-Dist: Pygments==2.19.2
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+ Requires-Dist: pyiceberg==0.9.1
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+ Requires-Dist: pynndescent==0.5.13
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+ Requires-Dist: pyparsing==3.2.3
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+ Requires-Dist: pysam==0.23.3
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+ Requires-Dist: python-dateutil==2.9.0.post0
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+ Requires-Dist: pytz==2025.2
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+ Requires-Dist: PyYAML==6.0.2
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+ Requires-Dist: pyzmq==27.0.2
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+ Requires-Dist: referencing==0.36.2
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+ Requires-Dist: requests==2.32.5
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+ Requires-Dist: rich==13.9.4
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+ Requires-Dist: rpds-py==0.27.1
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+ Requires-Dist: scanpy==1.11.4
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+ Requires-Dist: scikit-learn==1.7.1
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+ Requires-Dist: scikit-misc==0.5.1
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+ Requires-Dist: scipy==1.16.1
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+ Requires-Dist: seaborn==0.13.2
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+ Requires-Dist: session-info2==0.2.1
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+ Requires-Dist: six==1.17.0
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+ Requires-Dist: sortedcontainers==2.4.0
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+ Requires-Dist: SQLAlchemy==2.0.43
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+ Requires-Dist: stack_data==0.6.3
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+ Requires-Dist: statsmodels==0.14.5
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+ Requires-Dist: strictyaml==1.7.3
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+ Requires-Dist: sympy==1.14.0
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+ Requires-Dist: tables==3.10.2
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+ Requires-Dist: tenacity==9.1.2
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+ Requires-Dist: threadpoolctl==3.6.0
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+ Requires-Dist: torch==2.8.0
133
+ Requires-Dist: torchaudio==2.8.0
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+ Requires-Dist: torchvision==0.23.0
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+ Requires-Dist: tornado==6.5.2
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+ Requires-Dist: tqdm==4.67.1
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+ Requires-Dist: traitlets==5.14.3
138
+ Requires-Dist: triton==3.4.0
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+ Requires-Dist: typing_extensions==4.15.0
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+ Requires-Dist: typing-inspection==0.4.1
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+ Requires-Dist: tzdata==2025.2
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+ Requires-Dist: umap-learn==0.5.9.post2
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+ Requires-Dist: urllib3==2.5.0
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+ Requires-Dist: wcwidth==0.2.13
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+ Requires-Dist: wrapt==1.17.3
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+ Requires-Dist: xlsx2csv==0.8.4
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+ Requires-Dist: xlsxwriter==3.2.5
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+ Requires-Dist: zarr==3.1.2
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+ Requires-Dist: zipp==3.23.0
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+ Requires-Dist: zope.event==5.1.1
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+ Requires-Dist: zope.interface==7.2
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+ Dynamic: author
153
+ Dynamic: author-email
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+ Dynamic: requires-dist
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+ Dynamic: requires-python
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+ Dynamic: summary
scmultichat-0.1.0.dist-info/RECORD ADDED
@@ -0,0 +1,39 @@
1
+ MultiChat/__init__.py,sha256=FimBWeFZkWtcHp76dFlYXpqF49DzMTEgZ8rDEPsa6fk,234
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+ MultiChat/Analysis/Intra_strength.py,sha256=nP9rUgcmk3S84a-KayxdNL1OVYJbjHl3U33AxDVgd8c,62186
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+ MultiChat/Analysis/Processing.py,sha256=ZK38XoHcLrG7Db82XXk0C6u4aJZHfNe-JlzpqgX433U,6426
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+ MultiChat/Analysis/__init__.py,sha256=r6pAlFvu2hSvKxlqMX-CYofDt96ESUqlJPRFR--CWhk,54
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+ MultiChat/Heterogeneous_g_emb/__init__.py,sha256=HRcPrXt6f_TZUhc6aiRbzay7TTxS_rrt93XSPOV5NzQ,337
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+ MultiChat/Heterogeneous_g_emb/_settings.py,sha256=eqGMML6deLfg5tLZSdyP3xBXvD7N0M8CaCktPmi69NE,5150
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+ MultiChat/Heterogeneous_g_emb/_utils.py,sha256=klP30WolK7Bj_CWd341T7uukA97DlevfSAjR-9u0pmo,5089
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+ MultiChat/Heterogeneous_g_emb/_version.py,sha256=4IhULiQCZepM5JcGcijafBinwA7QfcWvCksEkYbUTZE,47
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+ MultiChat/Heterogeneous_g_emb/readwrite.py,sha256=4d4eAai9pGEWzFDL3Gck1QBdnrU_VT7VZtCddVGwdN4,8610
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+ MultiChat/Heterogeneous_g_emb/plotting/__init__.py,sha256=ivjz_4ilI-7uH-l0k1MwpcQW7vOVhdI5MEX9omvMvvA,284
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+ MultiChat/Heterogeneous_g_emb/plotting/_palettes.py,sha256=pn6ZqCD9XLvkME7RDm77GU5-ozVlj_5N92Rw3f0oryM,3596
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+ MultiChat/Heterogeneous_g_emb/plotting/_plot.py,sha256=s-d8Ov_FBMuWlMMKkD2Ssw5k98kh8Zugc53xil1r-SE,58392
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+ MultiChat/Heterogeneous_g_emb/plotting/_post_training.py,sha256=4xoCFkWHDGrRjS-LbzcYhvhxMD_MX7-5GbOmvgV9BpI,29885
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+ MultiChat/Heterogeneous_g_emb/plotting/_utils.py,sha256=zq4oYodVHQUaGgeo1u7fTK4QDgJ2RBrJsSOW9usBqY8,3597
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+ MultiChat/Heterogeneous_g_emb/preprocessing/__init__.py,sha256=l_YKGUMjp3CfqC0rPEC2Kg4LS3u0m1Gqdjqj4H3Hlew,413
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+ MultiChat/Heterogeneous_g_emb/preprocessing/_general.py,sha256=S1fx_lK4XfgjRfoMZf4Od8un-JANMJeESXTQAL36Pi0,2546
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+ MultiChat/Heterogeneous_g_emb/preprocessing/_pca.py,sha256=QZQ11uahtWJgcI0Vcg0QRhQzMeRDFPyFeCTr_cKVFRE,6484
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+ MultiChat/Heterogeneous_g_emb/preprocessing/_qc.py,sha256=tdZIF793Q9OxC_fIOArLuRybNal9t540FH2hEmWnfGw,30297
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+ MultiChat/Heterogeneous_g_emb/preprocessing/_utils.py,sha256=Zo9fKlfeTUJhZ-zaviUIWm6bu9I6bQJeDWKQMZsjq3Y,1798
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+ MultiChat/Heterogeneous_g_emb/preprocessing/_variable_genes.py,sha256=QrI3uTV3E6O-34edF2YJCS57oxxPllEj7R4Yf3nrN_w,2545
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+ MultiChat/Heterogeneous_g_emb/tools/__init__.py,sha256=JnBwNUmMKGqkgX5TffY83kRuPMp_A_Uywsl-SEjcL1s,387
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+ MultiChat/Heterogeneous_g_emb/tools/_gene_scores.py,sha256=YqSGuwpdHTc8uo-qFl716VSqD0VfySLMaxd7awjNmHA,12675
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+ MultiChat/Heterogeneous_g_emb/tools/_general.py,sha256=nMvN08pnDyzpTyjoRE4lpDi2J14J7buLDPZE5y-F5S4,2332
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+ MultiChat/Heterogeneous_g_emb/tools/_integration.py,sha256=5TaYuFN-QdwNSlrlh4jZEDb9uO7H0dzikoP6uUjv_kc,7499
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+ MultiChat/Heterogeneous_g_emb/tools/_pbg.py,sha256=1G2zQQqy1QDsJv-4vnE69tS9dJQaFsiOTuO7HDO5uJM,54404
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+ MultiChat/Heterogeneous_g_emb/tools/_post_training.py,sha256=h0O1fM10dNLEO-p3mHI7i2pfygl8-UCAA6Ak6isAjms,37962
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+ MultiChat/Heterogeneous_g_emb/tools/_umap.py,sha256=-lom7-WoeDDBfCXiLJEL-fvcUc3RJw_QijbfY_3azDk,1855
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+ MultiChat/Heterogeneous_g_emb/tools/_utils.py,sha256=6S1HGCdh2SDxlpriJZXToFTOBFRHhdbhJdAlziru78g,10847
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+ MultiChat/Model/Layers.py,sha256=A8w1De_Grtm4QjQcqnTirIl6TGjC_RD0Y2HUZ6iL_vU,3599
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+ MultiChat/Model/__init__.py,sha256=Egv_eklxxDwf1R07BYfs1Q0oaFNLMG1BDcX-958b_Mc,58
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+ MultiChat/Model/model_training.py,sha256=dkQkjor6mET9kfTTANA_f5UypYis-UkjudpAfTNV0e0,5225
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+ MultiChat/Model/modules.py,sha256=a6o6kANSOw7dRYbA2bgLrphh4vJThqSKOUr1SYoqkxk,2143
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+ MultiChat/Model/utilities.py,sha256=AyucTixKm4FaasN4jZzGoA4SsSl9ZDYWvdDO91dFoWA,9876
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+ MultiChat/Plot/Visualization.py,sha256=Uuyoguts1zB3zhZ6qFgf0nYF1qP9Ul9n0MQDafk0P5c,16302
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+ MultiChat/Plot/__init__.py,sha256=ntt5L3Rpq3buAf9y8UZrIMtnwSq3O-FLuLfJIn5KOpI,27
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+ scmultichat-0.1.0.dist-info/METADATA,sha256=DtINXA_K9MHMXVfJTLPj-Q6ADv9iKcuJGTGWFbY-Mys,4967
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+ scmultichat-0.1.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
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+ scmultichat-0.1.0.dist-info/top_level.txt,sha256=-3XcBbJ8DmBBKsT8BUk4-5Vx8HCfIN-fjLvzJYNFiis,10
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+ scmultichat-0.1.0.dist-info/RECORD,,
scmultichat-0.1.0.dist-info/WHEEL ADDED
@@ -0,0 +1,5 @@
1
+ Wheel-Version: 1.0
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+ Generator: setuptools (80.10.2)
3
+ Root-Is-Purelib: true
4
+ Tag: py3-none-any
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+
scmultichat-0.1.0.dist-info/top_level.txt ADDED
@@ -0,0 +1 @@
1
+ MultiChat