LICENSE.md
MANIFEST.in
README.md
requirements.txt
setup.py
commot/__init__.py
commot.egg-info/PKG-INFO
commot.egg-info/SOURCES.txt
commot.egg-info/dependency_links.txt
commot.egg-info/requires.txt
commot.egg-info/top_level.txt
commot/_optimal_transport/__init__.py
commot/_optimal_transport/_cot.py
commot/_optimal_transport/_unot.py
commot/_optimal_transport/_usot.py
commot/_utils/__init__.py
commot/_utils/_binarization.py
commot/_utils/_clustering.py
commot/_utils/_plotting.py
commot/_utils/_similarity.py
commot/_utils/plot_chord.R
commot/plotting/__init__.py
commot/plotting/_plotting.py
commot/preprocessing/__init__.py
commot/preprocessing/_infer_spatial.py
commot/preprocessing/_ligand_receptor_database.py
commot/preprocessing/_data/LRdatabase/CellChat/CellChatDB.ligrec.human.csv
commot/preprocessing/_data/LRdatabase/CellChat/CellChatDB.ligrec.mouse.csv
commot/preprocessing/_data/LRdatabase/CellChat/CellChatDB.ligrec.zebrafish.csv
commot/preprocessing/_data/LRdatabase/CellPhoneDB_v4.0/CellPhoneDBv4.0.human.csv
commot/preprocessing/_data/LRdatabase/CellPhoneDB_v4.0/CellPhoneDBv4.0.mouse.csv
commot/preprocessing/_data/LRdatabase/CellPhoneDB_v4.0/.ipynb_checkpoints/CellPhoneDBv4.0.human-checkpoint.csv
commot/preprocessing/_data/LRdatabase/CellPhoneDB_v4.0/.ipynb_checkpoints/Untitled-checkpoint.ipynb
commot/tools/__init__.py
commot/tools/_downstream_analysis.py
commot/tools/_spatial_communication.py
docs/Makefile
docs/conf.py
docs/index.rst
docs/make.bat
docs/_build/doctrees/environment.pickle
docs/_build/doctrees/index.doctree
docs/_build/doctrees/api/commot.pl.plot_cell_communication.doctree
docs/_build/doctrees/api/commot.pl.plot_cluster_communication_dotplot.doctree
docs/_build/doctrees/api/commot.pl.plot_cluster_communication_network.doctree
docs/_build/doctrees/api/commot.pl.plot_communication_dependent_genes.doctree
docs/_build/doctrees/api/commot.pl.plot_communication_impact.doctree
docs/_build/doctrees/api/commot.pp.filter_lr_database.doctree
docs/_build/doctrees/api/commot.pp.infer_spatial_information.doctree
docs/_build/doctrees/api/commot.pp.ligand_receptor_database.doctree
docs/_build/doctrees/api/commot.tl.cluster_communication.doctree
docs/_build/doctrees/api/commot.tl.cluster_communication_spatial_permutation.doctree
docs/_build/doctrees/api/commot.tl.cluster_position.doctree
docs/_build/doctrees/api/commot.tl.communication_deg_clustering.doctree
docs/_build/doctrees/api/commot.tl.communication_deg_detection.doctree
docs/_build/doctrees/api/commot.tl.communication_direction.doctree
docs/_build/doctrees/api/commot.tl.communication_impact.doctree
docs/_build/doctrees/api/commot.tl.communication_spatial_autocorrelation.doctree
docs/_build/doctrees/api/commot.tl.group_cell_communication.doctree
docs/_build/doctrees/api/commot.tl.group_cluster_communication.doctree
docs/_build/doctrees/api/commot.tl.group_communication_direction.doctree
docs/_build/doctrees/api/commot.tl.spatial_communication.doctree
docs/_build/doctrees/api/index.doctree
docs/_build/html/.buildinfo
docs/_build/html/genindex.html
docs/_build/html/index.html
docs/_build/html/objects.inv
docs/_build/html/py-modindex.html
docs/_build/html/search.html
docs/_build/html/searchindex.js
docs/_build/html/_images/cell_communication.png
docs/_build/html/_images/cluster_communication.png
docs/_build/html/_images/cluster_communication_dotplot.png
docs/_build/html/_images/communication_deg.png
docs/_build/html/_images/communication_impact.png
docs/_build/html/_sources/index.rst.txt
docs/_build/html/_sources/api/commot.pl.plot_cell_communication.rst.txt
docs/_build/html/_sources/api/commot.pl.plot_cluster_communication_dotplot.rst.txt
docs/_build/html/_sources/api/commot.pl.plot_cluster_communication_network.rst.txt
docs/_build/html/_sources/api/commot.pl.plot_communication_dependent_genes.rst.txt
docs/_build/html/_sources/api/commot.pl.plot_communication_impact.rst.txt
docs/_build/html/_sources/api/commot.pp.filter_lr_database.rst.txt
docs/_build/html/_sources/api/commot.pp.infer_spatial_information.rst.txt
docs/_build/html/_sources/api/commot.pp.ligand_receptor_database.rst.txt
docs/_build/html/_sources/api/commot.tl.cluster_communication.rst.txt
docs/_build/html/_sources/api/commot.tl.cluster_communication_spatial_permutation.rst.txt
docs/_build/html/_sources/api/commot.tl.cluster_position.rst.txt
docs/_build/html/_sources/api/commot.tl.communication_deg_clustering.rst.txt
docs/_build/html/_sources/api/commot.tl.communication_deg_detection.rst.txt
docs/_build/html/_sources/api/commot.tl.communication_direction.rst.txt
docs/_build/html/_sources/api/commot.tl.communication_impact.rst.txt
docs/_build/html/_sources/api/commot.tl.communication_spatial_autocorrelation.rst.txt
docs/_build/html/_sources/api/commot.tl.group_cell_communication.rst.txt
docs/_build/html/_sources/api/commot.tl.group_cluster_communication.rst.txt
docs/_build/html/_sources/api/commot.tl.group_communication_direction.rst.txt
docs/_build/html/_sources/api/commot.tl.spatial_communication.rst.txt
docs/_build/html/_sources/api/index.rst.txt
docs/_build/html/_static/_sphinx_javascript_frameworks_compat.js
docs/_build/html/_static/basic.css
docs/_build/html/_static/doctools.js
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docs/_build/html/_static/jquery-3.6.0.js
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docs/_build/html/api/commot.pl.plot_cell_communication.html
docs/_build/html/api/commot.pl.plot_cluster_communication_dotplot.html
docs/_build/html/api/commot.pl.plot_cluster_communication_network.html
docs/_build/html/api/commot.pl.plot_communication_dependent_genes.html
docs/_build/html/api/commot.pl.plot_communication_impact.html
docs/_build/html/api/commot.pp.filter_lr_database.html
docs/_build/html/api/commot.pp.infer_spatial_information.html
docs/_build/html/api/commot.pp.ligand_receptor_database.html
docs/_build/html/api/commot.tl.cluster_communication.html
docs/_build/html/api/commot.tl.cluster_communication_spatial_permutation.html
docs/_build/html/api/commot.tl.cluster_position.html
docs/_build/html/api/commot.tl.communication_deg_clustering.html
docs/_build/html/api/commot.tl.communication_deg_detection.html
docs/_build/html/api/commot.tl.communication_direction.html
docs/_build/html/api/commot.tl.communication_impact.html
docs/_build/html/api/commot.tl.communication_spatial_autocorrelation.html
docs/_build/html/api/commot.tl.group_cell_communication.html
docs/_build/html/api/commot.tl.group_cluster_communication.html
docs/_build/html/api/commot.tl.group_communication_direction.html
docs/_build/html/api/commot.tl.spatial_communication.html
docs/_build/html/api/index.html
docs/api/cell_communication.png
docs/api/cluster_communication.png
docs/api/cluster_communication_dotplot.png
docs/api/commot.pl.plot_cell_communication.rst
docs/api/commot.pl.plot_cluster_communication_dotplot.rst
docs/api/commot.pl.plot_cluster_communication_network.rst
docs/api/commot.pl.plot_communication_dependent_genes.rst
docs/api/commot.pl.plot_communication_impact.rst
docs/api/commot.pp.filter_lr_database.rst
docs/api/commot.pp.infer_spatial_information.rst
docs/api/commot.pp.ligand_receptor_database.rst
docs/api/commot.tl.cluster_communication.rst
docs/api/commot.tl.cluster_communication_spatial_permutation.rst
docs/api/commot.tl.cluster_position.rst
docs/api/commot.tl.communication_deg_clustering.rst
docs/api/commot.tl.communication_deg_detection.rst
docs/api/commot.tl.communication_direction.rst
docs/api/commot.tl.communication_impact.rst
docs/api/commot.tl.communication_spatial_autocorrelation.rst
docs/api/commot.tl.group_cell_communication.rst
docs/api/commot.tl.group_cluster_communication.rst
docs/api/commot.tl.group_communication_direction.rst
docs/api/commot.tl.spatial_communication.rst
docs/api/communication_deg.png
docs/api/communication_impact.png
docs/api/index.rst
tests/test_cluster_communication.py
tests/test_cluster_communication_spatial_permutation.py
tests/test_communication_direction.py
tests/test_spatial_communication.py