.codecov.yml
.flake8
.readthedocs.yml
.travis.yml
AUTHORS.rst
CONTRIBUTING.rst
LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
tox.ini
docs/Makefile
docs/source/conf.py
docs/source/documentutils.rst
docs/source/expansion.rst
docs/source/filters.rst
docs/source/generation.rst
docs/source/heat.rst
docs/source/index.rst
docs/source/installation.rst
docs/source/integration.rst
docs/source/mutation.rst
docs/source/selection.rst
docs/source/summary.rst
docs/source/utilities.rst
docs/source/algorithms/causalr.rst
docs/source/algorithms/epicom.rst
docs/source/algorithms/neurommsig.rst
docs/source/algorithms/rcr.rst
docs/source/algorithms/spia.rst
docs/source/assemblers/html.rst
docs/source/assemblers/ideogram.rst
src/pybel_tools/__init__.py
src/pybel_tools/assess_completeness.py
src/pybel_tools/chemistry.py
src/pybel_tools/definition_utils.py
src/pybel_tools/dict_manager.py
src/pybel_tools/document_utils.py
src/pybel_tools/generation.py
src/pybel_tools/node_utils.py
src/pybel_tools/pathway_assigner.py
src/pybel_tools/typing.py
src/pybel_tools/utils.py
src/pybel_tools/version.py
src/pybel_tools.egg-info/PKG-INFO
src/pybel_tools.egg-info/SOURCES.txt
src/pybel_tools.egg-info/dependency_links.txt
src/pybel_tools.egg-info/requires.txt
src/pybel_tools.egg-info/top_level.txt
src/pybel_tools.egg-info/zip-safe
src/pybel_tools/analysis/__init__.py
src/pybel_tools/analysis/causalr.py
src/pybel_tools/analysis/concordance.py
src/pybel_tools/analysis/heat.py
src/pybel_tools/analysis/mechanisms.py
src/pybel_tools/analysis/rcr.py
src/pybel_tools/analysis/spia.py
src/pybel_tools/analysis/sst.py
src/pybel_tools/analysis/epicom/__init__.py
src/pybel_tools/analysis/epicom/algorithm.py
src/pybel_tools/analysis/epicom/build.py
src/pybel_tools/analysis/epicom/models.py
src/pybel_tools/analysis/neurommsig/__init__.py
src/pybel_tools/analysis/neurommsig/__main__.py
src/pybel_tools/analysis/neurommsig/algorithm.py
src/pybel_tools/analysis/neurommsig/cli.py
src/pybel_tools/analysis/neurommsig/export.py
src/pybel_tools/assembler/__init__.py
src/pybel_tools/assembler/html/__init__.py
src/pybel_tools/assembler/html/assembler.py
src/pybel_tools/assembler/html/templates/base.html
src/pybel_tools/assembler/html/templates/compilation.html
src/pybel_tools/assembler/html/templates/index.html
src/pybel_tools/assembler/ideogram/__init__.py
src/pybel_tools/assembler/ideogram/assembler.py
src/pybel_tools/assembler/ideogram/templates/index.html
src/pybel_tools/assembler/ideogram/templates/render_with_javascript.js
src/pybel_tools/assembler/reified_graph/__init__.py
src/pybel_tools/assembler/reified_graph/assembler.py
src/pybel_tools/assembler/reified_graph/simple_assembler.py
src/pybel_tools/biogrammar/__init__.py
src/pybel_tools/biogrammar/double_edges.py
src/pybel_tools/filters/__init__.py
src/pybel_tools/filters/edge_filters.py
src/pybel_tools/filters/node_deletion.py
src/pybel_tools/filters/node_filters.py
src/pybel_tools/integration/__init__.py
src/pybel_tools/integration/overlay.py
src/pybel_tools/mutation/__init__.py
src/pybel_tools/mutation/bound.py
src/pybel_tools/mutation/collapse.py
src/pybel_tools/mutation/deletion.py
src/pybel_tools/mutation/expansion.py
src/pybel_tools/mutation/highlight.py
src/pybel_tools/mutation/inference.py
src/pybel_tools/mutation/metadata.py
src/pybel_tools/mutation/random.py
src/pybel_tools/selection/__init__.py
src/pybel_tools/selection/group_nodes.py
src/pybel_tools/selection/metapaths.py
src/pybel_tools/selection/paths.py
src/pybel_tools/selection/rewiring.py
src/pybel_tools/selection/search.py
src/pybel_tools/selection/utils.py
src/pybel_tools/summary/__init__.py
src/pybel_tools/summary/composite_summary.py
src/pybel_tools/summary/contradictions.py
src/pybel_tools/summary/edge_summary.py
src/pybel_tools/summary/error_summary.py
src/pybel_tools/summary/node_properties.py
src/pybel_tools/summary/provenance.py
src/pybel_tools/summary/stability.py
src/pybel_tools/summary/subgraph_summary.py
src/pybel_tools/summary/visualization.py
src/pybel_tools/validators/__init__.py
src/pybel_tools/validators/hgvs_validator.py
tests/__init__.py
tests/constants.py
tests/test_analysis.py
tests/test_analysis_stability.py
tests/test_causalr.py
tests/test_citation_utils.py
tests/test_heat.py
tests/test_integrate.py
tests/test_mapping.py
tests/test_node_utils.py
tests/test_reified_graph_assembler.py
tests/test_utils.py
tests/test_assemblers/__init__.py
tests/test_assemblers/test_summary_html.py
tests/test_mutation/__init__.py
tests/test_mutation/test_bound.py
tests/test_mutation/test_collapse.py
tests/test_mutation/test_enrich.py
tests/test_mutation/test_inference.py