.codecov.yml
.editorconfig
.gitignore
.pre-commit-config.yaml
.readthedocs.yml
MANIFEST.in
README.md
hatch.toml
pyproject.toml
app/main.py
ci/scripts/min-deps.py
ci/scripts/towncrier_automation.py
docs/Makefile
docs/community.md
docs/conf.py
docs/contributors.md
docs/index.md
docs/installation.md
docs/matplotlibrc
docs/news.md
docs/references.bib
docs/references.rst
docs/_static/img/gcell_logo.svg
docs/_templates/autosummary/class.rst
docs/api/celltype.md
docs/api/dna.md
docs/api/index.md
docs/api/pathway.md
docs/api/protein.md
docs/api/rna.md
docs/dev/code.md
docs/dev/documentation.md
docs/dev/getting-set-up.md
docs/dev/index.md
docs/dev/release.md
docs/dev/testing.md
docs/dev/versioning.md
docs/extensions/debug_docstrings.py
docs/extensions/function_images.py
docs/extensions/git_ref.py
docs/extensions/has_attr_test.py
docs/release-notes/+b2ad875a.doc.md
docs/release-notes/index.md
scripts/clean_build.sh
src/gcell/__init__.py
src/gcell/_logging.py
src/gcell/_settings.py
src/gcell/_version.py
src/gcell.egg-info/PKG-INFO
src/gcell.egg-info/SOURCES.txt
src/gcell.egg-info/dependency_links.txt
src/gcell.egg-info/requires.txt
src/gcell.egg-info/top_level.txt
src/gcell/cell/__init__.py
src/gcell/cell/celltype.py
src/gcell/cell/mutincell.py
src/gcell/config/__init__.py
src/gcell/config/config.py
src/gcell/config/local_interpret.yaml
src/gcell/config/s3_interpret.yaml
src/gcell/dna/__init__.py
src/gcell/dna/genome.py
src/gcell/dna/hocomoco.py
src/gcell/dna/motif.py
src/gcell/dna/motif_utils.py
src/gcell/dna/mutation.py
src/gcell/dna/nr_motif_v1.py
src/gcell/dna/nr_motif_v2.py
src/gcell/dna/sequence.py
src/gcell/dna/track.py
src/gcell/ontology/__init__.py
src/gcell/ontology/pathway.py
src/gcell/protein/__init__.py
src/gcell/protein/_math.py
src/gcell/protein/af2.py
src/gcell/protein/data.py
src/gcell/protein/interpro.py
src/gcell/protein/mutations.py
src/gcell/protein/protein.py
src/gcell/protein/stringdb.py
src/gcell/protein/uniprot.py
src/gcell/rna/__init__.py
src/gcell/rna/gencode.py
src/gcell/rna/gene.py
src/gcell/rna/gtf.py
src/gcell/utils/__init__.py
src/gcell/utils/causal_lib.py
src/gcell/utils/lingam.py
src/gcell/utils/lingam.r
src/gcell/utils/pdb_viewer.py
src/gcell/utils/s3.py
tests/test_annotation.py
tests/gcell/dna/test_nr_motif_v1.py
tests/gcell/protein/test_interpro.py
tests/gcell/protein/test_protein.py