.gitignore
LICENSE
README.rst
experiments-requirements.txt
pyproject.toml
requirements.txt
biPCA.egg-info/PKG-INFO
biPCA.egg-info/SOURCES.txt
biPCA.egg-info/dependency_links.txt
biPCA.egg-info/entry_points.txt
biPCA.egg-info/requires.txt
biPCA.egg-info/top_level.txt
bipca/__init__.py
bipca/base.py
bipca/bipca.py
bipca/bipca.py.save
bipca/command_line.py
bipca/data_examples.py
bipca/math.py
bipca/plotting.py
bipca/safe_basics.py
bipca/utils.py
bipca/_vendor/__init__.py
bipca/_vendor/pyalra/LICENSE
bipca/_vendor/pyalra/__init__.py
bipca/_vendor/pyalra/alra.py
bipca/_vendor/pyalra/choose_k.py
bipca/_vendor/pyalra/logging.py
bipca/_vendor/pychebfun/LICENSE
bipca/_vendor/pychebfun/__init__.py
bipca/_vendor/pychebfun/chebfun.py
bipca/_vendor/pychebfun/chebfun_init.py
bipca/_vendor/pychebfun/plotting.py
bipca/_vendor/pychebfun/polyfun.py
bipca/experiments/__init__.py
bipca/experiments/base.py
bipca/experiments/exceptions.py
bipca/experiments/experiments.py
bipca/experiments/normalizations.py
bipca/experiments/types.py
bipca/experiments/utils.py
bipca/experiments/datasets/__init__.py
bipca/experiments/datasets/allcools_preprocess.sh
bipca/experiments/datasets/base.py
bipca/experiments/datasets/datasets.py
bipca/experiments/datasets/modalities.py
bipca/experiments/datasets/plink_preprocess.sh
bipca/experiments/datasets/utils.py
bipca/experiments/figures/Figure1_Suppfig1.ipynb
bipca/experiments/figures/__init__.py
bipca/experiments/figures/base.py
bipca/experiments/figures/figures.py
bipca/experiments/figures/plotting_constants.py
bipca/experiments/figures/utils.py
doc/Makefile
doc/conf.py
doc/index.rst
doc/make.bat
doc/_static/numpy.css
doc/_templates/indexcontent.html
doc/_templates/indexsidebar.html
doc/_templates/layout.html
doc/_templates/searchbox.html
doc/_templates/autosummary/attribute.rst
doc/_templates/autosummary/base.rst
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doc/_templates/autosummary/method.rst
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doc/reference/bipca.rst
doc/reference/index.rst
doc/reference/math.rst
doc/reference/generated/bipca.math.SVD.PCA.rst
doc/reference/generated/bipca.math.SVD.S.rst
doc/reference/generated/bipca.math.SVD.U.rst
doc/reference/generated/bipca.math.SVD.V.rst
doc/reference/generated/bipca.math.SVD.algorithm.rst
doc/reference/generated/bipca.math.SVD.exact.rst
doc/reference/generated/bipca.math.SVD.fit.rst
doc/reference/generated/bipca.math.SVD.fit_transform.rst
doc/reference/generated/bipca.math.SVD.get_params.rst
doc/reference/generated/bipca.math.SVD.k.rst
doc/reference/generated/bipca.math.SVD.kwargs.rst
doc/reference/generated/bipca.math.SVD.n_components.rst
doc/reference/generated/bipca.math.SVD.rst
doc/reference/generated/bipca.math.SVD.set_params.rst
doc/reference/generated/bipca.math.SVD.svd.rst
doc/reference/generated/bipca.math.SVD.transform.rst
doc/reference/generated/bipca.math.Shrinker.fit.rst
doc/reference/generated/bipca.math.Shrinker.fit_transform.rst
doc/reference/generated/bipca.math.Shrinker.frobenius.rst
doc/reference/generated/bipca.math.Shrinker.get_params.rst
doc/reference/generated/bipca.math.Shrinker.hard.rst
doc/reference/generated/bipca.math.Shrinker.nuclear.rst
doc/reference/generated/bipca.math.Shrinker.operator.rst
doc/reference/generated/bipca.math.Shrinker.rst
doc/reference/generated/bipca.math.Shrinker.set_params.rst
doc/reference/generated/bipca.math.Shrinker.soft.rst
doc/reference/generated/bipca.math.Shrinker.transform.rst
doc/reference/generated/bipca.math.Sinkhorn.Z.rst
doc/reference/generated/bipca.math.Sinkhorn.fit.rst
doc/reference/generated/bipca.math.Sinkhorn.fit_transform.rst
doc/reference/generated/bipca.math.Sinkhorn.get_params.rst
doc/reference/generated/bipca.math.Sinkhorn.rst
doc/reference/generated/bipca.math.Sinkhorn.scale.rst
doc/reference/generated/bipca.math.Sinkhorn.set_params.rst
doc/reference/generated/bipca.math.Sinkhorn.transform.rst
doc/reference/generated/bipca.math.Sinkhorn.unscale.rst
tests/speedtest.py
tests/test_bipca.py
tests/test_command_line.py
tests/test_experiments.py
tests/test_math.py
tests/test_utils.py
tests/testing_utils.py
tests/test_data/__init__.py
tutorials/Figure1.png
tutorials/tutorial-0-quick_start.ipynb
tutorials/tutorial-1-pbmc_scrna_scanpy.ipynb