.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/changelog.md
docs/conf.py
docs/faq.md
docs/index.md
docs/installation.md
docs/license.md
docs/quickstart.md
docs/references.md
docs/requirements.txt
docs/statistical_guidance.md
docs/_static/css/custom.css
docs/api/index.md
docs/tutorials/index.md
docs/tutorials/t_ec_active_transcription.ipynb
docs/tutorials/t_ec_standalone_de_enrichment.ipynb
docs/tutorials/t_ga_active_transcription.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/real_data_template.py
examples/synthetic_active_transcription.py
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/enrich.py
src/scatrans/generate_gene_features.py
src/scatrans/pl.py
src/scatrans/pp_bias.py
src/scatrans/qc.py
src/scatrans/tl.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
src/scatrans/data/human_GRCh38_2024A_gene_features.parquet
src/scatrans/data/mouse_2020A_gene_features.parquet
tests/__init__.py
tests/conftest.py
tests/test_basic.py
tests/test_de_backends.py
tests/test_de_edge_cases.py
tests/test_enrich_api.py
tests/test_enrich_go.py
tests/test_pl_coverage.py
tests/test_pl_extended.py
tests/test_pp_bias_cli.py
tests/test_public_api.py
tests/test_regression_bugs.py
tests/test_small_sample_edges.py
tests/test_tl_coverage.py