├── .github └── workflows │ ├── cli-tests.yml │ ├── conventional-commits.yml │ ├── pre-commit.yml │ ├── publish-pypi.yml │ └── release-please.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── LICENSE.md ├── README.md ├── SECURITY.md ├── assets └── model_overview.png ├── conf └── inference_config.yaml ├── notebooks ├── celltype-classification-across-species.ipynb └── contextual-gene-embeddings.ipynb ├── preprocess ├── README.md ├── fasta_manifest_pep.json ├── get_stable_id_mapping.py ├── protein_embedding.py └── requirements.txt ├── pyproject.toml ├── src └── transcriptformer │ ├── __init__.py │ ├── cli │ ├── __init__.py │ ├── conf │ │ └── inference_config.yaml │ ├── download_artifacts.py │ ├── download_data.py │ └── inference.py │ ├── data │ ├── __init__.py │ ├── bulk_download.py │ ├── dataclasses.py │ └── dataloader.py │ ├── datasets.py │ ├── model │ ├── __init__.py │ ├── embedding_surgery.py │ ├── inference.py │ ├── layers.py │ ├── losses.py │ ├── masks.py │ └── model.py │ ├── tokenizer │ ├── __init__.py │ ├── tokenizer.py │ └── vocab.py │ └── utils │ ├── __init__.py │ └── utils.py └── test ├── __init__.py ├── conftest.py ├── data ├── chicken_val.h5ad ├── human_val.h5ad ├── mouse_val.h5ad └── reference_embeddings │ ├── embeddings_exemplar_mouse.h5ad │ ├── embeddings_metazoa_chicken.h5ad │ └── embeddings_sapiens_human.h5ad ├── test_cli.py ├── test_cli_integration.py ├── test_compare_emb.py ├── test_compare_umap.py ├── test_download_artifacts.py ├── test_download_data.py └── test_inference.py /.github/workflows/cli-tests.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/czi-ai/transcriptformer/HEAD/.github/workflows/cli-tests.yml -------------------------------------------------------------------------------- /.github/workflows/conventional-commits.yml: -------------------------------------------------------------------------------- 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