.gitignore
.pre-commit-config.yaml
.readthedocs.yml
LICENSE
README.rst
environment.yml
pypi.rst
pyproject.toml
requirements.txt
setup.py
.github/workflows/on-push.yml
cospar/__init__.py
cospar/datasets.py
cospar/hf.py
cospar/logging.py
cospar/pl.py
cospar/pp.py
cospar/settings.py
cospar/simulate.py
cospar/tl.py
cospar.egg-info/PKG-INFO
cospar.egg-info/SOURCES.txt
cospar.egg-info/dependency_links.txt
cospar.egg-info/requires.txt
cospar.egg-info/top_level.txt
cospar/help_functions/__init__.py
cospar/help_functions/_docs.py
cospar/help_functions/_help_functions_CoSpar.py
cospar/plotting/__init__.py
cospar/plotting/_clone.py
cospar/plotting/_gene.py
cospar/plotting/_map.py
cospar/plotting/_utils.py
cospar/preprocessing/__init__.py
cospar/preprocessing/_preprocessing.py
cospar/tmap/__init__.py
cospar/tmap/_tmap_core.py
cospar/tmap/_utils.py
cospar/tmap/map_reconstruction.py
cospar/tmap/optimal_transport.py
cospar/tool/__init__.py
cospar/tool/_clone.py
cospar/tool/_gene.py
cospar/tool/_map.py
cospar/tool/_utils.py
docs/Makefile
docs/make.bat
docs/requirements.txt
docs/source/20210120_bifurcation_model_static_barcoding.ipynb
docs/source/20210121_all_hematopoietic_data_v3.ipynb
docs/source/20210121_lung_data_v2.ipynb
docs/source/20210121_reprogramming_static_barcoding_v2.ipynb
docs/source/20210602_loading_data.ipynb
docs/source/20211010_clonal_analysis.ipynb
docs/source/20211010_map_analysis.ipynb
docs/source/20211010_map_inference.ipynb
docs/source/20211010_preprocessing.ipynb
docs/source/20220402_simulate_differentiation.ipynb
docs/source/about.rst
docs/source/api.rst
docs/source/conf.py
docs/source/getting_started.rst
docs/source/index.rst
docs/source/installation.rst
docs/source/release_note.rst
docs/source/.ipynb_checkpoints/20201121-Bifurcation_model_staticBC-CoSapr_basic-checkpoint.ipynb
docs/source/.ipynb_checkpoints/20210120-Bifurcation_model_dynamic_barcoding-checkpoint.ipynb
docs/source/.ipynb_checkpoints/20210120-Bifurcation_model_static_barcoding-checkpoint.ipynb
docs/source/.ipynb_checkpoints/20210121_all_hematopoietic_data-checkpoint.ipynb
docs/source/.ipynb_checkpoints/20210121_cospar_tutorial-checkpoint.ipynb
docs/source/.ipynb_checkpoints/20210121_lung_data-checkpoint.ipynb
docs/source/.ipynb_checkpoints/20210121_reprogramming_data_merge_tags-checkpoint.ipynb
docs/source/.ipynb_checkpoints/20210121_reprogramming_data_no_merge_tags-checkpoint.ipynb
docs/source/.ipynb_checkpoints/20210121_reprogramming_dynamic_barcoding-checkpoint.ipynb
docs/source/.ipynb_checkpoints/20210121_subsampled_hematopoietic_data-checkpoint.ipynb
docs/source/_ext/edit_on_github.py
docs/source/_static/colab-badge.svg
docs/source/_static/custom.css
docs/source/_static/nbviewer-badge.svg
docs/source/_templates/autosummary/base.rst
docs/source/_templates/autosummary/class.rst
tests/__init__.py
tests/context.py
tests/test_all.py
tests/data/cell_id.txt
tests/data/clonal_data_in_table_format.txt
tests/data/test_adata_preprocessed.h5ad