.flake8
.gitignore
.pre-commit-config.yaml
LICENSE
README.md
pyproject.toml
requirements-dev.txt
requirements.txt
setup.cfg
setup.py
.ci/check-requirements-cache.py
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.github/workflows/docs-test.yml
docs/.nojekyll
docs/Makefile
docs/cansig-for-python-coders.rst
docs/conf.py
docs/contributing.rst
docs/formatting-data.rst
docs/index.rst
docs/interpretation.rst
docs/make.bat
docs/pipeline-advanced.rst
docs/preprocessing.rst
docs/troubleshooting.rst
docs/assets/pipeline.png
docs/source/cansig.cluster.rst
docs/source/cansig.cnvanalysis.rst
docs/source/cansig.filesys.rst
docs/source/cansig.integration.base.rst
docs/source/cansig.integration.data.rst
docs/source/cansig.integration.module.rst
docs/source/cansig.integration.rst
docs/source/cansig.integration.training.rst
docs/source/cansig.interface.rst
docs/source/cansig.metaanalysis.rst
docs/source/cansig.models.rst
docs/source/cansig.plotting.rst
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src/__init__.py
src/cansig/__init__.py
src/cansig/api.py
src/cansig/filesys.py
src/cansig/gsea.py
src/cansig/logger.py
src/cansig/multirun.py
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src/cansig/_preprocessing/quality_control.py
src/cansig/_preprocessing/scoring.py
src/cansig/_preprocessing/subclonal.py
src/cansig/_preprocessing/utils.py
src/cansig/cluster/__init__.py
src/cansig/cluster/api.py
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src/cansig/cnvanalysis/__init__.py
src/cansig/cnvanalysis/differentialcnvs.py
src/cansig/integration/_CONSTANTS.py
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src/cansig/integration/model.py
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src/cansig/interface/cluster.py
src/cansig/metaanalysis/__init__.py
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src/cansig/metasignatures/api.py
src/cansig/metasignatures/clustering.py
src/cansig/metasignatures/utils.py
src/cansig/models/__init__.py
src/cansig/models/api.py
src/cansig/models/cansig.py
src/cansig/models/scvi.py
src/cansig/plotting/__init__.py
src/cansig/plotting/plotting.py
src/cansig/run/__init__.py
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src/cansig/run/format.py
src/cansig/run/heatmap.py
src/cansig/run/integration.py
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tests/preprocessing/utils.py