├── .cruft.json ├── .github └── workflows │ ├── deploy-docs.yml │ ├── pypi-publish.yml │ └── qc.yml ├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── docs ├── evaluations.md ├── functions.md ├── index.md ├── operation.md ├── setup.md └── troubleshooting.md ├── mkdocs.yml ├── notebooks ├── mixed_set_summarization.ipynb └── parse_msigdb.ipynb ├── poetry.lock ├── pyproject.toml ├── src └── talisman │ ├── __init__.py │ ├── cli.py │ ├── engines │ └── enrichment.py │ ├── evaluation │ ├── __init__.py │ ├── evaluation_engine.py │ └── resolver.py │ ├── prompts │ ├── __init__.py │ └── enrichment │ │ ├── __init__.py │ │ ├── gene_set_summarization.jinja2 │ │ ├── gene_set_summarization_with_p_values.jinja2 │ │ ├── gene_set_summarization_with_p_values_0.jinja2 │ │ ├── gene_set_summarization_with_p_values_1.jinja2 │ │ └── gene_set_summarization_with_p_values_2.jinja2 │ ├── streamlit │ └── talisman.py │ └── utils │ ├── __init__.py │ └── gene_set_utils.py ├── tests ├── __init__.py ├── input │ ├── genesets │ │ ├── EDS.yaml │ │ ├── FA.yaml │ │ ├── HALLMARK_ADIPOGENESIS.yaml │ │ ├── HALLMARK_ALLOGRAFT_REJECTION.yaml │ │ ├── HALLMARK_ANDROGEN_RESPONSE.yaml │ │ ├── HALLMARK_ANGIOGENESIS.yaml │ │ ├── HALLMARK_APICAL_JUNCTION.yaml │ │ ├── HALLMARK_APICAL_SURFACE.yaml │ │ ├── HALLMARK_APOPTOSIS.yaml │ │ ├── HALLMARK_BILE_ACID_METABOLISM.yaml │ │ ├── HALLMARK_CHOLESTEROL_HOMEOSTASIS.yaml │ │ ├── HALLMARK_COAGULATION.yaml │ │ ├── HALLMARK_COMPLEMENT.yaml │ │ ├── HALLMARK_DNA_REPAIR.yaml │ │ ├── HALLMARK_E2F_TARGETS.yaml │ │ ├── HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION.yaml │ │ ├── HALLMARK_ESTROGEN_RESPONSE_EARLY.yaml │ │ ├── HALLMARK_ESTROGEN_RESPONSE_LATE.yaml │ │ ├── HALLMARK_FATTY_ACID_METABOLISM.yaml │ │ ├── HALLMARK_G2M_CHECKPOINT.yaml │ │ ├── HALLMARK_GLYCOLYSIS.yaml │ │ ├── HALLMARK_HEDGEHOG_SIGNALING.yaml │ │ ├── HALLMARK_HEME_METABOLISM.yaml │ │ ├── HALLMARK_HYPOXIA.yaml │ │ ├── HALLMARK_IL2_STAT5_SIGNALING.yaml │ │ ├── HALLMARK_IL6_JAK_STAT3_SIGNALING.yaml │ │ ├── HALLMARK_INFLAMMATORY_RESPONSE.yaml │ │ ├── HALLMARK_INTERFERON_ALPHA_RESPONSE.yaml │ │ ├── HALLMARK_INTERFERON_GAMMA_RESPONSE.yaml │ │ ├── HALLMARK_KRAS_SIGNALING_DN.yaml │ │ ├── HALLMARK_KRAS_SIGNALING_UP.yaml │ │ ├── HALLMARK_MITOTIC_SPINDLE.yaml │ │ ├── HALLMARK_MTORC1_SIGNALING.yaml │ │ ├── HALLMARK_MYC_TARGETS_V1.yaml │ │ ├── HALLMARK_MYC_TARGETS_V2.yaml │ │ ├── HALLMARK_MYOGENESIS.yaml │ │ ├── HALLMARK_NOTCH_SIGNALING.yaml │ │ ├── HALLMARK_OXIDATIVE_PHOSPHORYLATION.yaml │ │ ├── HALLMARK_P53_PATHWAY.yaml │ │ ├── HALLMARK_PANCREAS_BETA_CELLS.yaml │ │ ├── HALLMARK_PEROXISOME.yaml │ │ ├── HALLMARK_PI3K_AKT_MTOR_SIGNALING.yaml │ │ ├── HALLMARK_PROTEIN_SECRETION.yaml │ │ ├── HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY.yaml │ │ ├── HALLMARK_SPERMATOGENESIS.yaml │ │ ├── HALLMARK_TGF_BETA_SIGNALING.yaml │ │ ├── HALLMARK_TNFA_SIGNALING_VIA_NFKB.yaml │ │ ├── HALLMARK_UNFOLDED_PROTEIN_RESPONSE.yaml │ │ ├── HALLMARK_UV_RESPONSE_DN.yaml │ │ ├── HALLMARK_UV_RESPONSE_UP.yaml │ │ ├── HALLMARK_WNT_BETA_CATENIN_SIGNALING.yaml │ │ ├── Yamanaka-TFs.yaml │ │ ├── amigo-example.yaml │ │ ├── bicluster_RNAseqDB_0.yaml │ │ ├── bicluster_RNAseqDB_1001.yaml │ │ ├── bicluster_RNAseqDB_1002.yaml │ │ ├── dopamine.yaml │ │ ├── meiosisI.yaml │ │ ├── mtorc1.yaml │ │ ├── peroxisome.yaml │ │ └── sensory-ataxia.yaml │ ├── go-nucleus.db │ ├── go-nucleus.halo.yaml │ ├── go-nucleus.json │ └── prompts │ │ ├── nedema-prompt.yaml │ │ └── prompts.yaml ├── integration │ ├── __init__.py │ ├── test_cli │ │ └── test_cli.py │ ├── test_evaluation │ │ ├── __init__.py │ │ └── test_eval_enrichment.py │ └── test_knowledge_engines │ │ ├── __init__.py │ │ └── test_enrichment.py ├── output │ └── gene_requests_cache.db └── unit │ ├── __init__.py │ ├── test_unit_cli.py │ └── test_utils │ ├── __init__.py │ └── test_gene_set_utils.py └── tox.ini /.cruft.json: -------------------------------------------------------------------------------- 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