.gitattributes
.gitignore
LICENSE
MANIFEST.in
README.md
environment.yml
release_notes.md
setup.cfg
setup.py
docker/Dockerfile
docker/build.sh
docs/Gemfile
docs/_config.yml
docs/citing_wot.html
docs/cli_documentation.html
docs/file_formats.md
docs/index.md
docs/source_code.html
docs/tutorial.html
docs/_data/examples.json
docs/_data/tools.json
docs/_includes/analytics.html
docs/_includes/head.html
docs/_includes/header.html
docs/_includes/navbar.html
docs/_layouts/base.html
docs/_layouts/documentation.html
docs/_layouts/home.html
docs/assets/css/style.scss
docs/images/Intro_fig.png
docs/images/Nbk1_fig.png
docs/images/Nbk2_fig.png
docs/images/Nbk3_fig.png
docs/images/Nbk4_fig.png
docs/images/Nbk5_fig.png
docs/images/Nbk6_fig.png
docs/images/Nbk7_fig.png
notebooks/Notebook-0-wot-setup.ipynb
notebooks/Notebook-1-FLE-cell_sets-gene_sets.ipynb
notebooks/Notebook-2-compute-transport-maps.ipynb
notebooks/Notebook-3-long-range-couplings.ipynb
notebooks/Notebook-4-ancestors-descendants-trajectories.ipynb
notebooks/Notebook-5-fate-matrices.ipynb
notebooks/Notebook-6-transition_table.ipynb
notebooks/Notebook-7-ot-validation.ipynb
notebooks/Notebook-8-predictive-TFs.ipynb
notebooks/command_line_example.sh
sdocs/conf.py
sdocs/index.rst
sdocs/requirements.txt
sdocs/wot.commands.rst
sdocs/wot.graphics.rst
sdocs/wot.grn.rst
sdocs/wot.io.rst
sdocs/wot.ot.rst
sdocs/wot.rst
sdocs/wot.simulate.rst
workflow/optimal_transport.wdl
workflow/optimal_transport_validation_parameter_sweep.wdl
wot/__init__.py
wot/__main__.py
wot/dataset_util.py
wot/gene_set_scores.py
wot/population.py
wot.egg-info/PKG-INFO
wot.egg-info/SOURCES.txt
wot.egg-info/dependency_links.txt
wot.egg-info/entry_points.txt
wot.egg-info/not-zip-safe
wot.egg-info/requires.txt
wot.egg-info/top_level.txt
wot/commands/__init__.py
wot/commands/cells_by_gene_set.py
wot/commands/census.py
wot/commands/convert_matrix.py
wot/commands/diff_exp.py
wot/commands/fates.py
wot/commands/gene_set_scores.py
wot/commands/optimal_transport.py
wot/commands/optimal_transport_validation.py
wot/commands/trajectory.py
wot/commands/trajectory_divergence.py
wot/commands/trajectory_trends.py
wot/commands/transition_table.py
wot/commands/util.py
wot/graphics/__init__.py
wot/graphics/color.py
wot/graphics/plot.py
wot/io/__init__.py
wot/io/io.py
wot/io/performance.py
wot/ot/__init__.py
wot/ot/initializer.py
wot/ot/optimal_transport.py
wot/ot/optimal_transport_validation.py
wot/ot/ot_model.py
wot/ot/util.py
wot/simulate/__init__.py
wot/simulate/simulate.py
wot/tmap/__init__.py
wot/tmap/chaining.py
wot/tmap/diff_exp.py
wot/tmap/trajectory_divergence.py
wot/tmap/transport_map_model.py
wot/tmap/util.py