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/baba2006_adapter.py
torchcell/adapters/baba2006_growth_adapter.py
torchcell/adapters/babu2014_adapter.py
torchcell/adapters/balakrishnan2022_adapter.py
torchcell/adapters/banerjee2024_titer_adapter.py
torchcell/adapters/banerjee2025_proteome_adapter.py
torchcell/adapters/baryshnikova2010_adapter.py
torchcell/adapters/bloom2019_adapter.py
torchcell/adapters/boocock2025_adapter.py
torchcell/adapters/borchert2023_adapter.py
torchcell/adapters/borchert2023_contrast_adapter.py
torchcell/adapters/borchert2024_adapter.py
torchcell/adapters/brunk2016_exometabolite_adapter.py
torchcell/adapters/brunk2016_metabolome_adapter.py
torchcell/adapters/brunk2016_proteome_adapter.py
torchcell/adapters/brunk2016_titer_adapter.py
torchcell/adapters/butland2008_adapter.py
torchcell/adapters/cachera2023_adapter.py
torchcell/adapters/caglar2017_doubling_time_adapter.py
torchcell/adapters/caglar2017_protein_fold_change_adapter.py
torchcell/adapters/caglar2017_proteome_adapter.py
torchcell/adapters/caglar2017_rnaseq_adapter.py
torchcell/adapters/campos2018_adapter.py
torchcell/adapters/campos2018_morphology_adapter.py
torchcell/adapters/carruthers2025_campaign_proteome_adapter.py
torchcell/adapters/carruthers2025_proteome_adapter.py
torchcell/adapters/carruthers2025_proteome_fold_change_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/dechiara2022_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/fitness_browser_ecoli_adapter.py
torchcell/adapters/fitness_browser_putida_adapter.py
torchcell/adapters/foo2014_adapter.py
torchcell/adapters/fuhrer2017_adapter.py
torchcell/adapters/gerdes2003_adapter.py
torchcell/adapters/girgis2009_adapter.py
torchcell/adapters/goodall2018_adapter.py
torchcell/adapters/goodall2018_graded_adapter.py
torchcell/adapters/gupta2024_adapter.py
torchcell/adapters/guzman2018_adapter.py
torchcell/adapters/hackett2020_adapter.py
torchcell/adapters/hale2024_adapter.py
torchcell/adapters/hawkins2020_adapter.py
torchcell/adapters/hillenmeyer2008_adapter.py
torchcell/adapters/hoepfner2014_adapter.py
torchcell/adapters/hu2007_adapter.py
torchcell/adapters/ishii2007_flux_adapter.py
torchcell/adapters/ishii2007_metabolome_adapter.py
torchcell/adapters/ishii2007_proteome_adapter.py
torchcell/adapters/jackson2020_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_growth_adapter.py
torchcell/adapters/lamoureux2023_public_k12_adapter.py
torchcell/adapters/li2014_adapter.py
torchcell/adapters/li2021_flux_adapter.py
torchcell/adapters/lian2019_adapter.py
torchcell/adapters/lim2022_adapter.py
torchcell/adapters/lim2025_proteome_adapter.py
torchcell/adapters/lim2025_proteome_fold_change_adapter.py
torchcell/adapters/lim2025_tolerance_adapter.py
torchcell/adapters/lopez2024_adapter.py
torchcell/adapters/menasalvas2025_adapter.py
torchcell/adapters/menasalvas2025_metabolite_growth_adapter.py
torchcell/adapters/menasalvas2025_metabolite_production_adapter.py
torchcell/adapters/menasalvas2025_proteome_adapter.py
torchcell/adapters/messner2021_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/muenzner2024_adapter.py
torchcell/adapters/mulleder2016_adapter.py
torchcell/adapters/mutalik2020_adapter.py
torchcell/adapters/nadal_ribelles2025_adapter.py
torchcell/adapters/nguessan2025_adapter.py
torchcell/adapters/nichols2011_adapter.py
torchcell/adapters/niu2019_adapter.py
torchcell/adapters/niu2019_pinene_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/parsons2006_adapter.py
torchcell/adapters/peter2018_adapter.py
torchcell/adapters/piotrowski2017_adapter.py
torchcell/adapters/potel2018_adapter.py
torchcell/adapters/price2018_ecoli_adapter.py
torchcell/adapters/price2018_ecoli_essentiality_adapter.py
torchcell/adapters/puddu2019_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/royet2025_adapter.py
torchcell/adapters/royet2025_graded_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_s23_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/teteneva2024_adapter.py
torchcell/adapters/thompson2019_valerolactam_growth_adapter.py
torchcell/adapters/thompson2019_valerolactam_titer_adapter.py
torchcell/adapters/tong2020_adapter.py
torchcell/adapters/vaishnav2022_adapter.py
torchcell/adapters/vanacloig2022_adapter.py
torchcell/adapters/volk2021_inhibitor_bioscreen_adapter.py
torchcell/adapters/wang2015_adapter.py
torchcell/adapters/wang2015_growth_adapter.py
torchcell/adapters/wang2018_adapter.py
torchcell/adapters/wang2018_gene_adapter.py
torchcell/adapters/wang2024_adapter.py
torchcell/adapters/wetmore2015_adapter.py
torchcell/adapters/wildenhain2015_adapter.py
torchcell/adapters/xue2025_adapter.py
torchcell/adapters/yoshida2012_adapter.py
torchcell/adapters/yoshikawa2009_adapter.py
torchcell/adapters/yunus2026_array_adapter.py
torchcell/adapters/yunus2026_differential_adapter.py
torchcell/adapters/yunus2026_knockdown_adapter.py
torchcell/adapters/yunus2026_panel_proteome_adapter.py
torchcell/adapters/yunus2026_titer_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/biofuel_titer_brunk2016_adapter.yaml
torchcell/adapters/conf/bloom2019_adapter.yaml
torchcell/adapters/conf/boocock2025_adapter.yaml
torchcell/adapters/conf/campaign_proteome_carruthers2025_adapter.yaml
torchcell/adapters/conf/carotenoid_ozaydin2013_adapter.yaml
torchcell/adapters/conf/caudal_pantranscriptome2024_adapter.yaml
torchcell/adapters/conf/cell_yield_dechiara2022_adapter.yaml
torchcell/adapters/conf/costanzo2021_adapter.yaml
torchcell/adapters/conf/crispr_magic_lian2019_adapter.yaml
torchcell/adapters/conf/crispr_pinene_tolerance_niu2019_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_gene_fitness_wang2018_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/crispri_panel_proteome_yunus2026_adapter.yaml
torchcell/adapters/conf/crispri_segregant_hale2024_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/doubling_time_caglar2017_adapter.yaml
torchcell/adapters/conf/doubling_time_dechiara2022_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_nichols2011_adapter.yaml
torchcell/adapters/conf/ecoli_env_chemgen_shiver2016_adapter.yaml
torchcell/adapters/conf/ecoli_env_chemgen_wang2024_adapter.yaml
torchcell/adapters/conf/ecoli_growth_rate_campos2018_adapter.yaml
torchcell/adapters/conf/ecoli_morphology_campos2018_adapter.yaml
torchcell/adapters/conf/env_chemgen_hoepfner2014_adapter.yaml
torchcell/adapters/conf/env_chemgen_parsons2006_adapter.yaml
torchcell/adapters/conf/env_chemgen_piotrowski2017_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/env_chemgen_yoshikawa2009_adapter.yaml
torchcell/adapters/conf/exometabolite_brunk2016_adapter.yaml
torchcell/adapters/conf/ffa_xue2025_adapter.yaml
torchcell/adapters/conf/fitness_contrast_borchert2023_adapter.yaml
torchcell/adapters/conf/flux_ishii2007_adapter.yaml
torchcell/adapters/conf/flux_li2021_adapter.yaml
torchcell/adapters/conf/gene_essentiality_baba2006_adapter.yaml
torchcell/adapters/conf/gene_essentiality_gerdes2003_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/genome_architecture_puddu2019_adapter.yaml
torchcell/adapters/conf/graded_gene_essentiality_goodall2018_adapter.yaml
torchcell/adapters/conf/graded_gene_essentiality_royet2025_adapter.yaml
torchcell/adapters/conf/growth_auc_rapp2026_adapter.yaml
torchcell/adapters/conf/growth_rate_choe2019_adapter.yaml
torchcell/adapters/conf/growth_rate_lamoureux2023_adapter.yaml
torchcell/adapters/conf/growth_rate_s23_schmidt2016_adapter.yaml
torchcell/adapters/conf/growth_rate_schmidt2016_adapter.yaml
torchcell/adapters/conf/growth_wang2015_adapter.yaml
torchcell/adapters/conf/growth_yield_baba2006_adapter.yaml
torchcell/adapters/conf/het_hillenmeyer2008_adapter.yaml
torchcell/adapters/conf/hom_hillenmeyer2008_adapter.yaml
torchcell/adapters/conf/induction_timecourse_hackett2020_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/isolate_growth_peter2018_adapter.yaml
torchcell/adapters/conf/isopentenol_titer_foo2014_adapter.yaml
torchcell/adapters/conf/isoprenol_selection_menasalvas2025_adapter.yaml
torchcell/adapters/conf/isoprenol_titer_banerjee2024_adapter.yaml
torchcell/adapters/conf/isoprenol_titer_carruthers2025_adapter.yaml
torchcell/adapters/conf/isoprenol_titer_desiqueira2025_adapter.yaml
torchcell/adapters/conf/isoprenol_titer_yunus2026_adapter.yaml
torchcell/adapters/conf/isoprenol_tolerance_lim2025_adapter.yaml
torchcell/adapters/conf/isoprenyl_acetate_titer_kang2026_adapter.yaml
torchcell/adapters/conf/lactam_growth_rate_thompson2019_adapter.yaml
torchcell/adapters/conf/life_cycle_dechiara2022_adapter.yaml
torchcell/adapters/conf/metabolite_dasilveira2014_adapter.yaml
torchcell/adapters/conf/metabolite_growth_menasalvas2025_adapter.yaml
torchcell/adapters/conf/metabolite_intensity_rapp2026_adapter.yaml
torchcell/adapters/conf/metabolite_production_menasalvas2025_adapter.yaml
torchcell/adapters/conf/metabolite_zelezniak2018_adapter.yaml
torchcell/adapters/conf/metabolome_brunk2016_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/microarray_score_hu2007_adapter.yaml
torchcell/adapters/conf/mismatch_crispri_fitness_hawkins2020_adapter.yaml
torchcell/adapters/conf/mota2024_adapter.yaml
torchcell/adapters/conf/mrna_fraction_balakrishnan2022_adapter.yaml
torchcell/adapters/conf/nadal_ribelles_perturbseq2025_adapter.yaml
torchcell/adapters/conf/nguessan2025_adapter.yaml
torchcell/adapters/conf/organic_acid_yoshida2012_adapter.yaml
torchcell/adapters/conf/phage_rbtnseq_mutalik2020_adapter.yaml
torchcell/adapters/conf/phosphosite_intensity_potel2018_adapter.yaml
torchcell/adapters/conf/pinene_fold_change_niu2019_adapter.yaml
torchcell/adapters/conf/pooled_promoter_expression_vaishnav2022_adapter.yaml
torchcell/adapters/conf/pputida_env_metal_tnseq_royet2025_adapter.yaml
torchcell/adapters/conf/promoter_reporter_mohiuddin2022_adapter.yaml
torchcell/adapters/conf/protein_fold_change_caglar2017_adapter.yaml
torchcell/adapters/conf/protein_synthesis_rate_li2014_adapter.yaml
torchcell/adapters/conf/protein_turnover_gupta2024_adapter.yaml
torchcell/adapters/conf/protein_turnover_muenzner2024_adapter.yaml
torchcell/adapters/conf/proteome_banerjee2025_adapter.yaml
torchcell/adapters/conf/proteome_brunk2016_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_fold_change_carruthers2025_adapter.yaml
torchcell/adapters/conf/proteome_fold_change_lim2025_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_menasalvas2025_adapter.yaml
torchcell/adapters/conf/proteome_messner2021_adapter.yaml
torchcell/adapters/conf/proteome_messner2023_adapter.yaml
torchcell/adapters/conf/proteome_mori2021_adapter.yaml
torchcell/adapters/conf/proteome_muenzner2024_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_fitness_browser_ecoli_adapter.yaml
torchcell/adapters/conf/rbtnseq_fitness_browser_putida_adapter.yaml
torchcell/adapters/conf/rbtnseq_price2018_ecoli_adapter.yaml
torchcell/adapters/conf/rbtnseq_teteneva2024_ecoli_adapter.yaml
torchcell/adapters/conf/rbtnseq_wetmore2015_ecoli_adapter.yaml
torchcell/adapters/conf/rnaseq_caglar2017_adapter.yaml
torchcell/adapters/conf/rnaseq_guzman2018_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_deletion_pseudobulk_jackson2020_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/adapters/conf/valerolactam_titer_thompson2019_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/candidates/__init__.py
torchcell/candidates/__main__.py
torchcell/candidates/cli.py
torchcell/candidates/findings.py
torchcell/candidates/gates.py
torchcell/candidates/ledger.py
torchcell/candidates/store.py
torchcell/candidates/verdict.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/experiment_types.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/construct.py
torchcell/datamodels/conversion.py
torchcell/datamodels/fitness_composite_conversion.py
torchcell/datamodels/gene_essentiality_to_fitness_conversion.py
torchcell/datamodels/genome_architecture_features.py
torchcell/datamodels/identity.py
torchcell/datamodels/interned_constant.py
torchcell/datamodels/media.py
torchcell/datamodels/morphology_features.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/fitness_browser.py
torchcell/datasets/fungal_up_down_transformer.py
torchcell/datasets/gene_alias_resolution.py
torchcell/datasets/genslm.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/baba2006.py
torchcell/datasets/ecoli/baba2006_growth.py
torchcell/datasets/ecoli/babu2014.py
torchcell/datasets/ecoli/balakrishnan2022.py
torchcell/datasets/ecoli/brunk2016.py
torchcell/datasets/ecoli/butland2008.py
torchcell/datasets/ecoli/caglar2017.py
torchcell/datasets/ecoli/caglar2017_doubling_time.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/fitness_browser_ecoli.py
torchcell/datasets/ecoli/foo2014.py
torchcell/datasets/ecoli/fuhrer2017.py
torchcell/datasets/ecoli/gerdes2003.py
torchcell/datasets/ecoli/girgis2009.py
torchcell/datasets/ecoli/goodall2018.py
torchcell/datasets/ecoli/gupta2024.py
torchcell/datasets/ecoli/guzman2018.py
torchcell/datasets/ecoli/hawkins2020.py
torchcell/datasets/ecoli/ishii2007.py
torchcell/datasets/ecoli/lamoureux2023.py
torchcell/datasets/ecoli/lamoureux2023_growth.py
torchcell/datasets/ecoli/lamoureux2023_public_k12.py
torchcell/datasets/ecoli/li2014.py
torchcell/datasets/ecoli/li2021.py
torchcell/datasets/ecoli/li2024.py
torchcell/datasets/ecoli/mohiuddin2022.py
torchcell/datasets/ecoli/mori2021.py
torchcell/datasets/ecoli/mutalik2020.py
torchcell/datasets/ecoli/nichols2011.py
torchcell/datasets/ecoli/niu2019.py
torchcell/datasets/ecoli/potel2018.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_s23_growth_rate.py
torchcell/datasets/ecoli/schmidt2016_srm.py
torchcell/datasets/ecoli/shiver2016.py
torchcell/datasets/ecoli/teteneva2024.py
torchcell/datasets/ecoli/tong2020.py
torchcell/datasets/ecoli/typas2008.py
torchcell/datasets/ecoli/wang2015.py
torchcell/datasets/ecoli/wang2015_growth.py
torchcell/datasets/ecoli/wang2018.py
torchcell/datasets/ecoli/wang2024.py
torchcell/datasets/ecoli/wetmore2015.py
torchcell/datasets/ecoli/zhang2015.py
torchcell/datasets/pputida/__init__.py
torchcell/datasets/pputida/banerjee2024.py
torchcell/datasets/pputida/banerjee2025.py
torchcell/datasets/pputida/borchert2023.py
torchcell/datasets/pputida/borchert2023_contrast.py
torchcell/datasets/pputida/borchert2024.py
torchcell/datasets/pputida/carruthers2025.py
torchcell/datasets/pputida/desiqueira2025.py
torchcell/datasets/pputida/fitness_browser_putida.py
torchcell/datasets/pputida/kang2026.py
torchcell/datasets/pputida/lim2022.py
torchcell/datasets/pputida/lim2025.py
torchcell/datasets/pputida/menasalvas2025.py
torchcell/datasets/pputida/royet2025.py
torchcell/datasets/pputida/thompson2019_valerolactam.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/boocock2025.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/dechiara2022.py
torchcell/datasets/scerevisiae/gene_name_reconcile.py
torchcell/datasets/scerevisiae/hackett2020.py
torchcell/datasets/scerevisiae/hale2024.py
torchcell/datasets/scerevisiae/hillenmeyer2008.py
torchcell/datasets/scerevisiae/hoepfner2014.py
torchcell/datasets/scerevisiae/hu2007.py
torchcell/datasets/scerevisiae/jackson2020.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/messner2021.py
torchcell/datasets/scerevisiae/messner2023.py
torchcell/datasets/scerevisiae/mormino2022.py
torchcell/datasets/scerevisiae/mota2024.py
torchcell/datasets/scerevisiae/muenzner2024.py
torchcell/datasets/scerevisiae/mulleder2016.py
torchcell/datasets/scerevisiae/nadal_ribelles2025.py
torchcell/datasets/scerevisiae/nguessan2025.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/parsons2006.py
torchcell/datasets/scerevisiae/peter2018.py
torchcell/datasets/scerevisiae/piotrowski2017.py
torchcell/datasets/scerevisiae/puddu2019.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/vaishnav2022.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/yoshikawa2009.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/csv_endpoint_gate.py
torchcell/knowledge_graphs/dataset_adapter_map.py
torchcell/knowledge_graphs/gene_interactions_scerevisae_kg.py
torchcell/knowledge_graphs/generate_adapter.py
torchcell/knowledge_graphs/generation_array.py
torchcell/knowledge_graphs/generation_image.py
torchcell/knowledge_graphs/head_ontology.py
torchcell/knowledge_graphs/incremental_import.py
torchcell/knowledge_graphs/kg_manifest.py
torchcell/knowledge_graphs/perturbation_lanes.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
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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/generation_tiers.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/manual_deposit.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/literature/zotero_add.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/genslm.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/models/genslm_assets/codon_wordlevel_69vocab.json
torchcell/models/genslm_assets/neox_2.5B.json
torchcell/models/genslm_assets/neox_250M.json
torchcell/models/genslm_assets/neox_25B.json
torchcell/models/genslm_assets/neox_25M.json
torchcell/models/genslm_assets/provenance.json
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_change.py
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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/natural_isolate.py
torchcell/sequence/plasmid.py
torchcell/sequence/construct/__init__.py
torchcell/sequence/construct/registry.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/ecoli/w3110.py
torchcell/sequence/genome/pputida/__init__.py
torchcell/sequence/genome/pputida/kt2440.py
torchcell/sequence/genome/scerevisiae/__init__.py
torchcell/sequence/genome/scerevisiae/ncbi.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/bacterial_morphology.py
torchcell/verification/common.py
torchcell/verification/construct_placement.py
torchcell/verification/environment_response.py
torchcell/verification/expression.py
torchcell/verification/expression_score.py
torchcell/verification/fitness.py
torchcell/verification/gene_essentiality.py
torchcell/verification/gene_interaction.py
torchcell/verification/genome_architecture.py
torchcell/verification/induction_timecourse.py
torchcell/verification/levels.py
torchcell/verification/metabolite.py
torchcell/verification/morphology.py
torchcell/verification/natural_isolate_genotype.py
torchcell/verification/natural_isolate_response.py
torchcell/verification/perturbation_families.py
torchcell/verification/phosphosite.py
torchcell/verification/pooled_sort_seq.py
torchcell/verification/product_titer.py
torchcell/verification/promoter_activity.py
torchcell/verification/protein.py
torchcell/verification/protein_fold_change.py
torchcell/verification/pseudobulk_umi_count.py
torchcell/verification/released.py
torchcell/verification/report.py
torchcell/verification/rnaseq.py
torchcell/verification/runners.py
torchcell/verification/segregant_expression.py
torchcell/verification/segregant_expression_reference_panel.py
torchcell/verification/segregant_growth.py
torchcell/verification/segregant_perturbation.py
torchcell/verification/sourced.py
torchcell/verification/synthetic_lethality.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