.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
README.md
SECURITY.md
conftest.py
conftest_fixtures.py
pyproject.toml
setup.cfg
.github/workflows/ci.yml
.github/workflows/publish.yml
docs/ROADMAP.md
docs/api_stability.md
docs/changelog.md
docs/conf.py
docs/domain_assumptions.md
docs/faq.md
docs/index.md
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docs/license.md
docs/method.md
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docs/requirements.txt
docs/statistical_guidance.md
docs/_static/method_routes_s1.png
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docs/api/index.md
docs/tutorials/index.md
docs/tutorials/t_ec_active_transcription.ipynb
docs/tutorials/t_ec_gene_upset.ipynb
docs/tutorials/t_ec_standalone_de_enrichment.ipynb
docs/tutorials/t_ga_active_transcription.ipynb
docs/tutorials/t_gse226488_partition_mechanism.ipynb
docs/tutorials/t_synthetic_visualization.ipynb
docs/user_guide/advanced.md
docs/user_guide/enrichment.md
docs/user_guide/gene_features.md
docs/user_guide/index.md
docs/user_guide/plotting.md
docs/user_guide/standalone_de.md
docs/user_guide/workflow.md
examples/memento_de_example.py
examples/partition_de_by_mechanism_example.py
examples/real_data_template.py
examples/select_annotate_workflow_example.py
examples/synthetic_active_transcription.py
packaging/bioconda/recipes/scatrans/meta.yaml
packaging/ecosystem-packages/meta.yaml
src/scatrans/__init__.py
src/scatrans/_de.py
src/scatrans/_permutation.py
src/scatrans/_utils.py
src/scatrans/_velocity.py
src/scatrans/_version.py
src/scatrans/generate_gene_features.py
src/scatrans/pl.py
src/scatrans/pp_bias.py
src/scatrans/qc.py
src/scatrans/data/DATA_LICENSES.md
src/scatrans/data/Hs_GO_Biological_Process_2026.txt
src/scatrans/data/Hs_KEGG_2026.txt
src/scatrans/data/Mm_GO_Biological_Process_2026.txt
src/scatrans/data/Mm_KEGG_2026.txt
src/scatrans/data/Mus_musculus.GRCm39.115_gene_features.parquet
src/scatrans/data/README.md
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src/scatrans/data/mouse_2020A_gene_features.parquet
src/scatrans/enrich/__init__.py
src/scatrans/enrich/_data.py
src/scatrans/enrich/compare.py
src/scatrans/enrich/gsea.py
src/scatrans/enrich/ora.py
src/scatrans/enrich/report.py
src/scatrans/enrich/simplify.py
src/scatrans/tl/__init__.py
src/scatrans/tl/_common.py
src/scatrans/tl/active.py
src/scatrans/tl/adaptive.py
src/scatrans/tl/bias.py
src/scatrans/tl/de.py
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src/scatrans/tl/filter.py
src/scatrans/tl/mechanism.py
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