.codecov.yml
.coveragerc
.readthedocs.yml
.travis.yml
AUTHORS.rst
CONTRIBUTING.rst
LICENSE
MANIFEST.in
README.rst
requirements.txt
setup.cfg
setup.py
tox.ini
docs/Makefile
docs/source/cli.rst
docs/source/cmpa.rst
docs/source/comparison.rst
docs/source/conf.py
docs/source/documentutils.rst
docs/source/expansion.rst
docs/source/filters.rst
docs/source/generation.rst
docs/source/index.rst
docs/source/installation.rst
docs/source/integration.rst
docs/source/ioutils.rst
docs/source/lexer.rst
docs/source/mutation.rst
docs/source/orthology.rst
docs/source/pipeline.rst
docs/source/selection.rst
docs/source/stability.rst
docs/source/summary.rst
docs/source/utilities.rst
docs/source/visualization.rst
src/pybel_tools/__init__.py
src/pybel_tools/__main__.py
src/pybel_tools/citation_utils.py
src/pybel_tools/cli.py
src/pybel_tools/comparison.py
src/pybel_tools/constants.py
src/pybel_tools/generation.py
src/pybel_tools/ioutils.py
src/pybel_tools/lexer.py
src/pybel_tools/ols_utils.py
src/pybel_tools/orthology.py
src/pybel_tools/pipeline.py
src/pybel_tools/query.py
src/pybel_tools/utils.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/entry_points.txt
src/pybel_tools.egg-info/requires.txt
src/pybel_tools.egg-info/top_level.txt
src/pybel_tools/analysis/__init__.py
src/pybel_tools/analysis/chemical_enrichment.py
src/pybel_tools/analysis/cmpa.py
src/pybel_tools/analysis/concordance.py
src/pybel_tools/analysis/mechanisms.py
src/pybel_tools/analysis/rcr.py
src/pybel_tools/analysis/sst.py
src/pybel_tools/analysis/stability.py
src/pybel_tools/analysis/neurommsig/__init__.py
src/pybel_tools/analysis/neurommsig/export.py
src/pybel_tools/analysis/neurommsig/neurommsig.py
src/pybel_tools/biogrammar/__init__.py
src/pybel_tools/biogrammar/binding_domains.py
src/pybel_tools/biogrammar/direct_interactions.py
src/pybel_tools/biogrammar/hgvs_validation.py
src/pybel_tools/biogrammar/kinases.py
src/pybel_tools/biogrammar/reactions.py
src/pybel_tools/biogrammar/snp_impact.py
src/pybel_tools/definition_utils/__init__.py
src/pybel_tools/definition_utils/summary_dependent.py
src/pybel_tools/definition_utils/summary_independent.py
src/pybel_tools/document_utils/__init__.py
src/pybel_tools/document_utils/document_utils.py
src/pybel_tools/document_utils/utils.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/filters/node_selection.py
src/pybel_tools/integration/__init__.py
src/pybel_tools/integration/overlay.py
src/pybel_tools/integration/description/__init__.py
src/pybel_tools/integration/description/go_annotator.py
src/pybel_tools/integration/description/hgnc.py
src/pybel_tools/integration/description/node_annotator.py
src/pybel_tools/mutation/__init__.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/mutation/utils.py
src/pybel_tools/selection/__init__.py
src/pybel_tools/selection/group_nodes.py
src/pybel_tools/selection/induce_subgraph.py
src/pybel_tools/selection/leaves.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/serialization/__init__.py
src/pybel_tools/serialization/functional.py
src/pybel_tools/summary/__init__.py
src/pybel_tools/summary/edge_summary.py
src/pybel_tools/summary/error_summary.py
src/pybel_tools/summary/export.py
src/pybel_tools/summary/node_properties.py
src/pybel_tools/summary/provenance.py
src/pybel_tools/summary/subgraph_summary.py
src/pybel_tools/visualization/__init__.py
src/pybel_tools/visualization/inline.py
src/pybel_tools/visualization/utils.py
src/pybel_tools/visualization/visualization.py
src/pybel_tools/visualization/templates/graph_template.html
src/pybel_tools/visualization/templates/pybel_vis.js
tests/__init__.py
tests/constants.py
tests/test_analysis_stability.py
tests/test_citation_utils.py
tests/test_cmpa.py
tests/test_diff.py
tests/test_expand_neighborhood.py
tests/test_integrate.py
tests/test_mapping.py
tests/test_mutation.py
tests/test_mutation_inference.py
tests/test_orthology.py
tests/test_processing.py
tests/test_query.py
tests/test_serialize_functional.py
tests/test_sst.py
tests/test_utils.py
tests/resources/RGD_ORTHOLOGS.txt
tests/resources/orthology.tsv