MANIFEST.in
README.md
pyproject.toml
env/requirements.txt
env/requirements_dependent.txt
torchcell/__init__.py
torchcell/__version__.py
torchcell/api_keys.py
torchcell/build_telemetry.py
torchcell/endpoint_http.py
torchcell/fast_csv.py
torchcell/py.typed
torchcell/timestamp.py
torchcell/torchcell.mplstyle
torchcell.egg-info/PKG-INFO
torchcell.egg-info/SOURCES.txt
torchcell.egg-info/dependency_links.txt
torchcell.egg-info/entry_points.txt
torchcell.egg-info/requires.txt
torchcell.egg-info/top_level.txt
torchcell/adapters/__init__.py
torchcell/adapters/auesukaree2009_adapter.py
torchcell/adapters/babu2014_adapter.py
torchcell/adapters/banerjee2025_proteome_adapter.py
torchcell/adapters/baryshnikova2010_adapter.py
torchcell/adapters/bloom2019_adapter.py
torchcell/adapters/borchert2023_adapter.py
torchcell/adapters/borchert2024_adapter.py
torchcell/adapters/butland2008_adapter.py
torchcell/adapters/cachera2023_adapter.py
torchcell/adapters/caglar2017_proteome_adapter.py
torchcell/adapters/caglar2017_rnaseq_adapter.py
torchcell/adapters/campos2018_adapter.py
torchcell/adapters/carruthers2025_proteome_adapter.py
torchcell/adapters/carruthers2025_titer_adapter.py
torchcell/adapters/caudal2024_adapter.py
torchcell/adapters/cell_adapter.py
torchcell/adapters/choe2019_growth_rate_adapter.py
torchcell/adapters/choe2019_tf_knockout_adapter.py
torchcell/adapters/choe2025_adapter.py
torchcell/adapters/cooper2010_adapter.py
torchcell/adapters/costanzo2016_adapter.py
torchcell/adapters/costanzo2021_adapter.py
torchcell/adapters/cui2018_adapter.py
torchcell/adapters/dasilveira2014_adapter.py
torchcell/adapters/desiqueira2025_proteome_adapter.py
torchcell/adapters/desiqueira2025_proteome_log10_percent_adapter.py
torchcell/adapters/desiqueira2025_proteome_percent_adapter.py
torchcell/adapters/desiqueira2025_titer_adapter.py
torchcell/adapters/fang2025_adapter.py
torchcell/adapters/foo2014_adapter.py
torchcell/adapters/fuhrer2017_adapter.py
torchcell/adapters/girgis2009_adapter.py
torchcell/adapters/goodall2018_adapter.py
torchcell/adapters/gupta2024_adapter.py
torchcell/adapters/hillenmeyer2008_adapter.py
torchcell/adapters/hoepfner2014_adapter.py
torchcell/adapters/ishii2007_flux_adapter.py
torchcell/adapters/ishii2007_metabolome_adapter.py
torchcell/adapters/ishii2007_proteome_adapter.py
torchcell/adapters/kang2026_adapter.py
torchcell/adapters/kemmeren2014_adapter.py
torchcell/adapters/kuzmin2018_adapter.py
torchcell/adapters/kuzmin2020_adapter.py
torchcell/adapters/lamoureux2023_adapter.py
torchcell/adapters/lamoureux2023_public_k12_adapter.py
torchcell/adapters/lian2019_adapter.py
torchcell/adapters/lim2022_adapter.py
torchcell/adapters/lim2025_proteome_adapter.py
torchcell/adapters/lim2025_tolerance_adapter.py
torchcell/adapters/lopez2024_adapter.py
torchcell/adapters/menasalvas2025_adapter.py
torchcell/adapters/messner2023_adapter.py
torchcell/adapters/mohiuddin2022_adapter.py
torchcell/adapters/mori2021_adapter.py
torchcell/adapters/mormino2022_adapter.py
torchcell/adapters/mota2024_adapter.py
torchcell/adapters/mulleder2016_adapter.py
torchcell/adapters/mutalik2020_adapter.py
torchcell/adapters/nadal_ribelles2025_adapter.py
torchcell/adapters/oduibhir2014_adapter.py
torchcell/adapters/ohnuki2018_adapter.py
torchcell/adapters/ohnuki2022_adapter.py
torchcell/adapters/ohya2005_adapter.py
torchcell/adapters/ozaydin2013_adapter.py
torchcell/adapters/price2018_ecoli_adapter.py
torchcell/adapters/price2018_ecoli_essentiality_adapter.py
torchcell/adapters/rachwalski2024_adapter.py
torchcell/adapters/rapp2026_adapter.py
torchcell/adapters/rapp2026_growth_adapter.py
torchcell/adapters/rapp2026_intensity_adapter.py
torchcell/adapters/rapp2026_targeted_adapter.py
torchcell/adapters/rousset2018_adapter.py
torchcell/adapters/sameith2015_adapter.py
torchcell/adapters/schastnaya2021_adapter.py
torchcell/adapters/schmidt2016_adapter.py
torchcell/adapters/schmidt2016_growth_rate_adapter.py
torchcell/adapters/schmidt2016_srm_set1_adapter.py
torchcell/adapters/schmidt2016_srm_set2_adapter.py
torchcell/adapters/sgd_adapter.py
torchcell/adapters/shiver2016_adapter.py
torchcell/adapters/smith2006_adapter.py
torchcell/adapters/smith2016_adapter.py
torchcell/adapters/synth_leth_db_adapter.py
torchcell/adapters/tong2020_adapter.py
torchcell/adapters/vanacloig2022_adapter.py
torchcell/adapters/volk2021_inhibitor_bioscreen_adapter.py
torchcell/adapters/wang2015_adapter.py
torchcell/adapters/wang2018_adapter.py
torchcell/adapters/wildenhain2015_adapter.py
torchcell/adapters/xue2025_adapter.py
torchcell/adapters/yoshida2012_adapter.py
torchcell/adapters/yunus2026_array_adapter.py
torchcell/adapters/yunus2026_differential_adapter.py
torchcell/adapters/yunus2026_knockdown_adapter.py
torchcell/adapters/zelezniak2018_adapter.py
torchcell/adapters/conf/__init__.py
torchcell/adapters/conf/amino_acid_cooper2010_adapter.yaml
torchcell/adapters/conf/amino_acid_mulleder2016_adapter.yaml
torchcell/adapters/conf/auesukaree2009_adapter.yaml
torchcell/adapters/conf/betaxanthin_cachera2023_adapter.yaml
torchcell/adapters/conf/bloom2019_adapter.yaml
torchcell/adapters/conf/carotenoid_ozaydin2013_adapter.yaml
torchcell/adapters/conf/caudal_pantranscriptome2024_adapter.yaml
torchcell/adapters/conf/costanzo2021_adapter.yaml
torchcell/adapters/conf/crispr_magic_lian2019_adapter.yaml
torchcell/adapters/conf/crispri_array_yunus2026_adapter.yaml
torchcell/adapters/conf/crispri_chemgen_choe2025_adapter.yaml
torchcell/adapters/conf/crispri_chemgen_smith2016_adapter.yaml
torchcell/adapters/conf/crispri_cross_rachwalski2024_adapter.yaml
torchcell/adapters/conf/crispri_differential_proteome_yunus2026_adapter.yaml
torchcell/adapters/conf/crispri_guide_ffa_enrichment_fang2025_adapter.yaml
torchcell/adapters/conf/crispri_guide_fitness_wang2018_adapter.yaml
torchcell/adapters/conf/crispri_knockdown_cui2018_adapter.yaml
torchcell/adapters/conf/crispri_knockdown_yunus2026_adapter.yaml
torchcell/adapters/conf/crispri_mormino2022_adapter.yaml
torchcell/adapters/conf/default.yaml
torchcell/adapters/conf/dm_microarray_sameith2015_adapter.yaml
torchcell/adapters/conf/dmf_costanzo2016_adapter.yaml
torchcell/adapters/conf/dmf_kuzmin2018_adapter.yaml
torchcell/adapters/conf/dmf_kuzmin2020_adapter.yaml
torchcell/adapters/conf/dmi_costanzo2016_adapter.yaml
torchcell/adapters/conf/dmi_kuzmin2018_adapter.yaml
torchcell/adapters/conf/dmi_kuzmin2020_adapter.yaml
torchcell/adapters/conf/ecoli_carbon_source_tong2020_adapter.yaml
torchcell/adapters/conf/ecoli_crispri_rousset2018_adapter.yaml
torchcell/adapters/conf/ecoli_env_chemgen_girgis2009_adapter.yaml
torchcell/adapters/conf/ecoli_env_chemgen_shiver2016_adapter.yaml
torchcell/adapters/conf/ecoli_growth_rate_campos2018_adapter.yaml
torchcell/adapters/conf/env_chemgen_hoepfner2014_adapter.yaml
torchcell/adapters/conf/env_chemgen_smith2006_adapter.yaml
torchcell/adapters/conf/env_chemgen_vanacloig2022_adapter.yaml
torchcell/adapters/conf/env_chemgen_wang2015_adapter.yaml
torchcell/adapters/conf/env_chemgen_wildenhain2015_adapter.yaml
torchcell/adapters/conf/ffa_xue2025_adapter.yaml
torchcell/adapters/conf/flux_ishii2007_adapter.yaml
torchcell/adapters/conf/gene_essentiality_goodall2018_adapter.yaml
torchcell/adapters/conf/gene_essentiality_price2018_ecoli_adapter.yaml
torchcell/adapters/conf/gene_essentiality_sgd_adapter.yaml
torchcell/adapters/conf/gene_interaction_babu2014_adapter.yaml
torchcell/adapters/conf/gene_interaction_butland2008_adapter.yaml
torchcell/adapters/conf/growth_auc_rapp2026_adapter.yaml
torchcell/adapters/conf/growth_rate_choe2019_adapter.yaml
torchcell/adapters/conf/growth_rate_schmidt2016_adapter.yaml
torchcell/adapters/conf/het_hillenmeyer2008_adapter.yaml
torchcell/adapters/conf/hom_hillenmeyer2008_adapter.yaml
torchcell/adapters/conf/inhibitor_bioscreen_volk2021_adapter.yaml
torchcell/adapters/conf/isobutanol_screen_lopez2024_adapter.yaml
torchcell/adapters/conf/isobutanol_validated_lopez2024_adapter.yaml
torchcell/adapters/conf/isopentenol_titer_foo2014_adapter.yaml
torchcell/adapters/conf/isoprenol_selection_menasalvas2025_adapter.yaml
torchcell/adapters/conf/isoprenol_titer_carruthers2025_adapter.yaml
torchcell/adapters/conf/isoprenol_titer_desiqueira2025_adapter.yaml
torchcell/adapters/conf/isoprenol_tolerance_lim2025_adapter.yaml
torchcell/adapters/conf/isoprenyl_acetate_titer_kang2026_adapter.yaml
torchcell/adapters/conf/metabolite_dasilveira2014_adapter.yaml
torchcell/adapters/conf/metabolite_intensity_rapp2026_adapter.yaml
torchcell/adapters/conf/metabolite_zelezniak2018_adapter.yaml
torchcell/adapters/conf/metabolome_fuhrer2017_adapter.yaml
torchcell/adapters/conf/metabolome_ishii2007_adapter.yaml
torchcell/adapters/conf/metabolome_rapp2026_adapter.yaml
torchcell/adapters/conf/metabolome_schastnaya2021_adapter.yaml
torchcell/adapters/conf/microarray_kemmeren2014_adapter.yaml
torchcell/adapters/conf/mota2024_adapter.yaml
torchcell/adapters/conf/nadal_ribelles_perturbseq2025_adapter.yaml
torchcell/adapters/conf/organic_acid_yoshida2012_adapter.yaml
torchcell/adapters/conf/phage_rbtnseq_mutalik2020_adapter.yaml
torchcell/adapters/conf/promoter_reporter_mohiuddin2022_adapter.yaml
torchcell/adapters/conf/protein_turnover_gupta2024_adapter.yaml
torchcell/adapters/conf/proteome_banerjee2025_adapter.yaml
torchcell/adapters/conf/proteome_caglar2017_adapter.yaml
torchcell/adapters/conf/proteome_carruthers2025_adapter.yaml
torchcell/adapters/conf/proteome_desiqueira2025_adapter.yaml
torchcell/adapters/conf/proteome_ishii2007_adapter.yaml
torchcell/adapters/conf/proteome_lim2025_adapter.yaml
torchcell/adapters/conf/proteome_log10_percent_desiqueira2025_adapter.yaml
torchcell/adapters/conf/proteome_messner2023_adapter.yaml
torchcell/adapters/conf/proteome_mori2021_adapter.yaml
torchcell/adapters/conf/proteome_percent_desiqueira2025_adapter.yaml
torchcell/adapters/conf/proteome_schmidt2016_adapter.yaml
torchcell/adapters/conf/proteome_srm_set1_schmidt2016_adapter.yaml
torchcell/adapters/conf/proteome_srm_set2_schmidt2016_adapter.yaml
torchcell/adapters/conf/proteome_zelezniak2018_adapter.yaml
torchcell/adapters/conf/putida_precise321_lim2022_adapter.yaml
torchcell/adapters/conf/rbtnseq_borchert2023_adapter.yaml
torchcell/adapters/conf/rbtnseq_borchert2024_adapter.yaml
torchcell/adapters/conf/rbtnseq_price2018_ecoli_adapter.yaml
torchcell/adapters/conf/rnaseq_caglar2017_adapter.yaml
torchcell/adapters/conf/rnaseq_lamoureux2023_adapter.yaml
torchcell/adapters/conf/rnaseq_public_k12_lamoureux2023_adapter.yaml
torchcell/adapters/conf/scmd_ohnuki2018_adapter.yaml
torchcell/adapters/conf/scmd_ohnuki2022_adapter.yaml
torchcell/adapters/conf/scmd_ohya2005_adapter.yaml
torchcell/adapters/conf/sm_microarray_sameith2015_adapter.yaml
torchcell/adapters/conf/smf_baryshnikova2010_adapter.yaml
torchcell/adapters/conf/smf_costanzo2016_adapter.yaml
torchcell/adapters/conf/smf_kuzmin2018_adapter.yaml
torchcell/adapters/conf/smf_kuzmin2020_adapter.yaml
torchcell/adapters/conf/smf_oduibhir2014_adapter.yaml
torchcell/adapters/conf/synth_lethality_yeast_synth_leth_db_adapter.yaml
torchcell/adapters/conf/synth_rescue_yeast_synth_leth_db_adapter.yaml
torchcell/adapters/conf/targeted_metabolome_rapp2026_adapter.yaml
torchcell/adapters/conf/tf_knockout_growth_choe2019_adapter.yaml
torchcell/adapters/conf/tmf_kuzmin2018_adapter.yaml
torchcell/adapters/conf/tmf_kuzmin2020_adapter.yaml
torchcell/adapters/conf/tmi_kuzmin2018_adapter.yaml
torchcell/adapters/conf/tmi_kuzmin2020_adapter.yaml
torchcell/artifacts/__init__.py
torchcell/artifacts/__main__.py
torchcell/artifacts/deposit.py
torchcell/artifacts/ref.py
torchcell/artifacts/resolve.py
torchcell/artifacts/tiers.py
torchcell/artifacts/walk.py
torchcell/cell/__init__.py
torchcell/data/__init__.py
torchcell/data/aggregate.py
torchcell/data/cell_data.py
torchcell/data/data.py
torchcell/data/deduplicate.py
torchcell/data/embedding.py
torchcell/data/experiment_dataset.py
torchcell/data/genotype_aggregate.py
torchcell/data/graph_processor.py
torchcell/data/hetero_data.py
torchcell/data/label_policy.py
torchcell/data/label_table.py
torchcell/data/mean_experiment_deduplicate.py
torchcell/data/neo4j_cell.py
torchcell/data/neo4j_preprocessed_cell.py
torchcell/data/neo4j_preprocessed_cell_full_masks.py
torchcell/data/neo4j_query_raw.py
torchcell/database/__init__.py
torchcell/database/browser_style.py
torchcell/database/build_command.py
torchcell/database/build_dataset_lmdb.py
torchcell/database/connection.py
torchcell/database/directory_setup.py
torchcell/database/tcdb.py
torchcell/datamodels/__init__.py
torchcell/datamodels/calmorph_labels.py
torchcell/datamodels/compound_identity.py
torchcell/datamodels/compound_identity_curate.py
torchcell/datamodels/compound_identity_table.json
torchcell/datamodels/conversion.py
torchcell/datamodels/fitness_composite_conversion.py
torchcell/datamodels/gene_essentiality_to_fitness_conversion.py
torchcell/datamodels/identity.py
torchcell/datamodels/interned_constant.py
torchcell/datamodels/media.py
torchcell/datamodels/ontology_checks.py
torchcell/datamodels/pydant.py
torchcell/datamodels/schema.py
torchcell/datamodels/strain_background.py
torchcell/datamodels/synthetic_lethality_to_fitness_conversion.py
torchcell/datamodules/__init__.py
torchcell/datamodules/cell.py
torchcell/datamodules/lazy_collate.py
torchcell/datamodules/perturbation_subset.py
torchcell/datasets/__init__.py
torchcell/datasets/artifact.py
torchcell/datasets/bacteria_common.py
torchcell/datasets/client.py
torchcell/datasets/codon_frequency.py
torchcell/datasets/codon_language_model.py
torchcell/datasets/dataset_registry.py
torchcell/datasets/esm2.py
torchcell/datasets/fungal_up_down_transformer.py
torchcell/datasets/node_embedding_builder.py
torchcell/datasets/nucleotide_transformer.py
torchcell/datasets/one_hot_gene.py
torchcell/datasets/protT5.py
torchcell/datasets/random_embedding.py
torchcell/datasets/server.py
torchcell/datasets/sgd_gene_graph.py
torchcell/datasets/ecoli/__init__.py
torchcell/datasets/ecoli/babu2014.py
torchcell/datasets/ecoli/butland2008.py
torchcell/datasets/ecoli/caglar2017.py
torchcell/datasets/ecoli/cai2023.py
torchcell/datasets/ecoli/campos2018.py
torchcell/datasets/ecoli/choe2019_growth_rate.py
torchcell/datasets/ecoli/choe2025.py
torchcell/datasets/ecoli/cui2018.py
torchcell/datasets/ecoli/fang2025.py
torchcell/datasets/ecoli/foo2014.py
torchcell/datasets/ecoli/fuhrer2017.py
torchcell/datasets/ecoli/girgis2009.py
torchcell/datasets/ecoli/goodall2018.py
torchcell/datasets/ecoli/gupta2024.py
torchcell/datasets/ecoli/ishii2007.py
torchcell/datasets/ecoli/lamoureux2023.py
torchcell/datasets/ecoli/lamoureux2023_public_k12.py
torchcell/datasets/ecoli/mohiuddin2022.py
torchcell/datasets/ecoli/mori2021.py
torchcell/datasets/ecoli/mutalik2020.py
torchcell/datasets/ecoli/price2018.py
torchcell/datasets/ecoli/rachwalski2024.py
torchcell/datasets/ecoli/rapp2026.py
torchcell/datasets/ecoli/rapp2026_platforms.py
torchcell/datasets/ecoli/rousset2018.py
torchcell/datasets/ecoli/schastnaya2021.py
torchcell/datasets/ecoli/schmidt2016.py
torchcell/datasets/ecoli/schmidt2016_growth_rate.py
torchcell/datasets/ecoli/schmidt2016_srm.py
torchcell/datasets/ecoli/shiver2016.py
torchcell/datasets/ecoli/tong2020.py
torchcell/datasets/ecoli/wang2015.py
torchcell/datasets/ecoli/wang2018.py
torchcell/datasets/ecoli/wetmore2015.py
torchcell/datasets/pputida/__init__.py
torchcell/datasets/pputida/banerjee2025.py
torchcell/datasets/pputida/borchert2023.py
torchcell/datasets/pputida/borchert2024.py
torchcell/datasets/pputida/carruthers2025.py
torchcell/datasets/pputida/desiqueira2025.py
torchcell/datasets/pputida/kang2026.py
torchcell/datasets/pputida/lim2022.py
torchcell/datasets/pputida/lim2025.py
torchcell/datasets/pputida/menasalvas2025.py
torchcell/datasets/pputida/yunus2026.py
torchcell/datasets/private_torchcell/__init__.py
torchcell/datasets/private_torchcell/bioscreen.py
torchcell/datasets/private_torchcell/volk2021_inhibitor_bioscreen.py
torchcell/datasets/private_torchcell/volk2021_sources.py
torchcell/datasets/scerevisiae/__init__.py
torchcell/datasets/scerevisiae/auesukaree2009.py
torchcell/datasets/scerevisiae/baryshnikova2010.py
torchcell/datasets/scerevisiae/bloom2019.py
torchcell/datasets/scerevisiae/cachera2023.py
torchcell/datasets/scerevisiae/caudal2024.py
torchcell/datasets/scerevisiae/cooper2010.py
torchcell/datasets/scerevisiae/costanzo2016.py
torchcell/datasets/scerevisiae/costanzo2021.py
torchcell/datasets/scerevisiae/dasilveira2014.py
torchcell/datasets/scerevisiae/gene_name_reconcile.py
torchcell/datasets/scerevisiae/hillenmeyer2008.py
torchcell/datasets/scerevisiae/hoepfner2014.py
torchcell/datasets/scerevisiae/kemmeren2014.py
torchcell/datasets/scerevisiae/kuzmin2018.py
torchcell/datasets/scerevisiae/kuzmin2020.py
torchcell/datasets/scerevisiae/lian2019.py
torchcell/datasets/scerevisiae/lopez2024.py
torchcell/datasets/scerevisiae/messner2023.py
torchcell/datasets/scerevisiae/mormino2022.py
torchcell/datasets/scerevisiae/mota2024.py
torchcell/datasets/scerevisiae/mulleder2016.py
torchcell/datasets/scerevisiae/nadal_ribelles2025.py
torchcell/datasets/scerevisiae/oduibhir2014.py
torchcell/datasets/scerevisiae/ohnuki2018.py
torchcell/datasets/scerevisiae/ohnuki2022.py
torchcell/datasets/scerevisiae/ohya2005.py
torchcell/datasets/scerevisiae/ozaydin2013.py
torchcell/datasets/scerevisiae/sameith2015.py
torchcell/datasets/scerevisiae/sgd.py
torchcell/datasets/scerevisiae/smith2006.py
torchcell/datasets/scerevisiae/smith2016.py
torchcell/datasets/scerevisiae/spell.py
torchcell/datasets/scerevisiae/synth_leth_db.py
torchcell/datasets/scerevisiae/vanacloig2022.py
torchcell/datasets/scerevisiae/wildenhain2015.py
torchcell/datasets/scerevisiae/xue2025.py
torchcell/datasets/scerevisiae/yeastphenome.py
torchcell/datasets/scerevisiae/yoshida2012.py
torchcell/datasets/scerevisiae/zelezniak2018.py
torchcell/experiments/003-fit-int/scripts/plot_ppi_reg_rcm.py
torchcell/graph/__init__.py
torchcell/graph/graph.py
torchcell/graph/sgd.py
torchcell/graph/validation/__init__.py
torchcell/graph/validation/locus_related/__init__.py
torchcell/graph/validation/locus_related/locus.py
torchcell/knowledge_graphs/__init__.py
torchcell/knowledge_graphs/build_time_projection.py
torchcell/knowledge_graphs/create_kg.py
torchcell/knowledge_graphs/create_scerevisiae_kg.py
torchcell/knowledge_graphs/create_scerevisiae_kg_small.py
torchcell/knowledge_graphs/dataset_adapter_map.py
torchcell/knowledge_graphs/gene_interactions_scerevisae_kg.py
torchcell/knowledge_graphs/head_ontology.py
torchcell/knowledge_graphs/incremental_import.py
torchcell/knowledge_graphs/kg_manifest.py
torchcell/knowledge_graphs/release_snapshot.py
torchcell/knowledge_graphs/releases.py
torchcell/knowledge_graphs/subset.py
torchcell/knowledge_graphs/conf/__init__.py
torchcell/knowledge_graphs/conf/calmorph_ohya2005_kg.yaml
torchcell/knowledge_graphs/conf/default.yaml
torchcell/knowledge_graphs/conf/dmf_costanzo2016_kg.yaml
torchcell/knowledge_graphs/conf/dmf_kuzmin2018_kg.yaml
torchcell/knowledge_graphs/conf/dmf_kuzmin2020_kg.yaml
torchcell/knowledge_graphs/conf/dmi_costanzo2016_kg.yaml
torchcell/knowledge_graphs/conf/dmi_kuzmin2018_kg.yaml
torchcell/knowledge_graphs/conf/dmi_kuzmin2020_kg.yaml
torchcell/knowledge_graphs/conf/gene_essentiality_sgd.yaml
torchcell/knowledge_graphs/conf/kg.yaml
torchcell/knowledge_graphs/conf/kg_bacteria.yaml
torchcell/knowledge_graphs/conf/kg_bench_bloom.yaml
torchcell/knowledge_graphs/conf/kg_bench_expr.yaml
torchcell/knowledge_graphs/conf/kg_bench_ladder.yaml
torchcell/knowledge_graphs/conf/kg_full.yaml
torchcell/knowledge_graphs/conf/kg_increment.yaml
torchcell/knowledge_graphs/conf/kg_selected_costanzo_doubles.yaml
torchcell/knowledge_graphs/conf/kg_small.yaml
torchcell/knowledge_graphs/conf/kg_uncapped.yaml
torchcell/knowledge_graphs/conf/scerevisiae_global_kg.yaml
torchcell/knowledge_graphs/conf/scerevisiae_small_global_kg.yaml
torchcell/knowledge_graphs/conf/smf_costanzo2016_kg.yaml
torchcell/knowledge_graphs/conf/smf_kuzmin2018_kg.yaml
torchcell/knowledge_graphs/conf/smf_kuzmin2020_kg.yaml
torchcell/knowledge_graphs/conf/synth_lethality_yeast_synth_leth_db.yaml
torchcell/knowledge_graphs/conf/synth_rescue_yeast_synth_leth_db.yaml
torchcell/knowledge_graphs/conf/tmf_kuzmin2018_kg.yaml
torchcell/knowledge_graphs/conf/tmf_kuzmin2020_kg.yaml
torchcell/knowledge_graphs/conf/tmi_kuzmin2018_kg.yaml
torchcell/knowledge_graphs/conf/tmi_kuzmin2020_kg.yaml
torchcell/knowledge_graphs/conf/tmi_tmf_kg.yaml
torchcell/knowledge_graphs/conf/gene_sets/sameith_double_pairs.txt
torchcell/knowledge_graphs/queries/__init__.py
torchcell/knowledge_graphs/queries/amino_acid_betaxanthin.cql
torchcell/knowledge_graphs/queries/essentiality_smf.cql
torchcell/knowledge_graphs/queries/expression_proteome_morphology.cql
torchcell/knowledge_graphs/queries/solid_growth_025.cql
torchcell/knowledge_graphs/supported_queries/__init__.py
torchcell/knowledge_graphs/supported_queries/__main__.py
torchcell/knowledge_graphs/supported_queries/check.py
torchcell/knowledge_graphs/supported_queries/cypher_deps.py
torchcell/knowledge_graphs/supported_queries/registry.json
torchcell/knowledge_graphs/supported_queries/registry.py
torchcell/literature/__init__.py
torchcell/literature/_run_mineru.py
torchcell/literature/annotations.py
torchcell/literature/backfill.py
torchcell/literature/bib.py
torchcell/literature/bib_store.py
torchcell/literature/calmorph.py
torchcell/literature/capture.py
torchcell/literature/capture_si.py
torchcell/literature/citation_keys.py
torchcell/literature/extract.py
torchcell/literature/manifest.py
torchcell/literature/ocr.py
torchcell/literature/provenance.py
torchcell/literature/reocr_si.py
torchcell/literature/retrieve.py
torchcell/literature/scanned.py
torchcell/literature/server.py
torchcell/literature/si_data.py
torchcell/literature/sync.py
torchcell/literature/zotero.py
torchcell/loader/__init__.py
torchcell/loader/cpu_experiment_loader.py
torchcell/loader/dense_padding_data_loader.py
torchcell/losses/__init__.py
torchcell/losses/dango.py
torchcell/losses/dcell.py
torchcell/losses/diffusion_loss.py
torchcell/losses/distributional.py
torchcell/losses/isomorphic_cell_loss.py
torchcell/losses/list_mle.py
torchcell/losses/logcosh.py
torchcell/losses/mle_dist_supcr.py
torchcell/losses/mle_wasserstein.py
torchcell/losses/multi_dim_nan_tolerant.py
torchcell/losses/point_dist_graph_reg.py
torchcell/metabolism/__init__.py
torchcell/metabolism/betaxanthin.py
torchcell/metabolism/constraints.py
torchcell/metabolism/enzyme_kinetics.py
torchcell/metabolism/flux_layer.py
torchcell/metabolism/media.py
torchcell/metabolism/parameters.py
torchcell/metabolism/pathway.py
torchcell/metabolism/yeast_GEM.py
torchcell/models/__init__.py
torchcell/models/act.py
torchcell/models/cell_graph_transformer.py
torchcell/models/cell_graph_transformer_metabolism.py
torchcell/models/dango.py
torchcell/models/dcell.py
torchcell/models/dcell_opt.py
torchcell/models/deep_set.py
torchcell/models/diffusion_decoder.py
torchcell/models/equivariant_cell_graph_transformer.py
torchcell/models/esm2.py
torchcell/models/fungal_up_down_transformer.py
torchcell/models/gpu_edge_mask_generator.py
torchcell/models/hetero_cell_bipartite_dango.py
torchcell/models/hetero_cell_bipartite_dango_diff_gi.py
torchcell/models/hetero_cell_bipartite_dango_gi.py
torchcell/models/hetero_cell_bipartite_dango_gi_lazy.py
torchcell/models/hetero_cell_nsa_retry.py
torchcell/models/linear.py
torchcell/models/llm.py
torchcell/models/mlp.py
torchcell/models/norm.py
torchcell/models/nucleotide_transformer.py
torchcell/models/protT5.py
torchcell/models/self_attention_deep_set.py
torchcell/nn/__init__.py
torchcell/nn/hetero_nsa.py
torchcell/nn/masked_attention_block.py
torchcell/nn/masked_gin_conv.py
torchcell/nn/nsa_encoder.py
torchcell/nn/self_attention_block.py
torchcell/nn/stoichiometric_hypergraph_conv.py
torchcell/ontology/__init__.py
torchcell/ontology/mermaid_diagram.py
torchcell/ontology/tc_ontology.py
torchcell/paper/__init__.py
torchcell/paper/ontology_graph.py
torchcell/paper/ontology_svg.py
torchcell/paper/signal.py
torchcell/paper/tables.py
torchcell/profiling/__init__.py
torchcell/profiling/timing.py
torchcell/provenance/__init__.py
torchcell/provenance/build_manifest.py
torchcell/provenance/schema_deps.py
torchcell/provenance/schema_impact.py
torchcell/scheduler/__init__.py
torchcell/scheduler/cosine_annealing_warmup.py
torchcell/scratch/cell_batch_overfit_visualization.py
torchcell/scratch/cell_graph_transformer_demo.py
torchcell/scratch/cell_graph_transformer_metabolism_demo.py
torchcell/scratch/compare_lazy_vs_subgraph.py
torchcell/scratch/cpu_performance_benchmark.py
torchcell/scratch/dango_demo.py
torchcell/scratch/dcell_opt_demo.py
torchcell/scratch/delete_0.py
torchcell/scratch/delete_00.py
torchcell/scratch/delete_1.py
torchcell/scratch/equivariant_cell_graph_transformer_demo.py
torchcell/scratch/hetero_cell_bipartite_dango_demo.py
torchcell/scratch/hetero_cell_bipartite_dango_diff_gi_demo.py
torchcell/scratch/hetero_cell_bipartite_dango_gi_lazy_demo.py
torchcell/scratch/hetero_cell_nsa_retry_demo.py
torchcell/scratch/linear_demo.py
torchcell/scratch/load_batch.py
torchcell/scratch/load_batch_004.py
torchcell/scratch/load_batch_005.py
torchcell/scratch/load_batch_006_perturbation.py
torchcell/scratch/load_lazy_batch_006.py
torchcell/scratch/load_neigbor_batch_006.py
torchcell/scratch/neo4j_cell_demo.py
torchcell/scratch/neo4j_preprocessed_cell_demo.py
torchcell/scratch/neo4j_query_speed.py
torchcell/scratch/neo4j_utils_query_speed.py
torchcell/scratch/profile_data_loading.py
torchcell/scratch/rustworkx_comparison.py
torchcell/scratch/sameith2015_demo.py
torchcell/scratch/save_reference_baseline.py
torchcell/scratch/spell_demo.py
torchcell/scratch/stoichiometric_hypergraph_conv_demo.py
torchcell/scratch/verify_lazy_equivalence.py
torchcell/sequence/__init__.py
torchcell/sequence/data.py
torchcell/sequence/db_connection.py
torchcell/sequence/plasmid.py
torchcell/sequence/genome/__init__.py
torchcell/sequence/genome/bacterial.py
torchcell/sequence/genome/base.py
torchcell/sequence/genome/registry.py
torchcell/sequence/genome/ecoli/__init__.py
torchcell/sequence/genome/ecoli/k12.py
torchcell/sequence/genome/ecoli/rel606.py
torchcell/sequence/genome/pputida/__init__.py
torchcell/sequence/genome/pputida/kt2440.py
torchcell/sequence/genome/scerevisiae/__init__.py
torchcell/sequence/genome/scerevisiae/s288c.py
torchcell/sga/__init__.py
torchcell/sga/assay.py
torchcell/sga/cellpose_seg.py
torchcell/sga/image.py
torchcell/sga/io.py
torchcell/sga/models.py
torchcell/sga/normalize.py
torchcell/sga/register.py
torchcell/sga/score.py
torchcell/sga/viz.py
torchcell/trainers/__init__.py
torchcell/trainers/dcell_regression.py
torchcell/trainers/dcell_regression_slim.py
torchcell/trainers/int_dango.py
torchcell/trainers/int_dcell.py
torchcell/trainers/int_hetero_cell.py
torchcell/trainers/int_transformer_cell.py
torchcell/trainers/neo_regression.py
torchcell/trainers/simple_linear_regression.py
torchcell/transforms/__init__.py
torchcell/transforms/coo_regression_to_classification.py
torchcell/transforms/hetero_to_dense_mask.py
torchcell/transforms/regression_to_classification.py
torchcell/utils/__init__.py
torchcell/utils/file_lock.py
torchcell/utils/paths.py
torchcell/utils/utils.py
torchcell/verification/__init__.py
torchcell/verification/common.py
torchcell/verification/environment_response.py
torchcell/verification/expression.py
torchcell/verification/fitness.py
torchcell/verification/levels.py
torchcell/verification/metabolite.py
torchcell/verification/morphology.py
torchcell/verification/product_titer.py
torchcell/verification/promoter_activity.py
torchcell/verification/protein.py
torchcell/verification/report.py
torchcell/verification/rnaseq.py
torchcell/verification/runners.py
torchcell/verification/segregant_growth.py
torchcell/verification/sourced.py
torchcell/verification/visual_score.py
torchcell/viz/__init__.py
torchcell/viz/fitness.py
torchcell/viz/genetic_interaction_score.py
torchcell/viz/graph_recovery.py
torchcell/viz/transformer_diagnostics.py
torchcell/viz/visual_graph_degen.py
torchcell/viz/visual_regression.py