All modules for which code is available
- torchcell.adapters.auesukaree2009_adapter
- torchcell.adapters.baryshnikova2010_adapter
- torchcell.adapters.bloom2019_adapter
- torchcell.adapters.cachera2023_adapter
- torchcell.adapters.caudal2024_adapter
- torchcell.adapters.cell_adapter
- torchcell.adapters.cooper2010_adapter
- torchcell.adapters.costanzo2016_adapter
- torchcell.adapters.costanzo2021_adapter
- torchcell.adapters.dasilveira2014_adapter
- torchcell.adapters.hillenmeyer2008_adapter
- torchcell.adapters.hoepfner2014_adapter
- torchcell.adapters.kemmeren2014_adapter
- torchcell.adapters.kuzmin2018_adapter
- torchcell.adapters.kuzmin2020_adapter
- torchcell.adapters.lian2019_adapter
- torchcell.adapters.lopez2024_adapter
- torchcell.adapters.messner2023_adapter
- torchcell.adapters.mormino2022_adapter
- torchcell.adapters.mota2024_adapter
- torchcell.adapters.mulleder2016_adapter
- torchcell.adapters.nadal_ribelles2025_adapter
- torchcell.adapters.oduibhir2014_adapter
- torchcell.adapters.ohnuki2018_adapter
- torchcell.adapters.ohnuki2022_adapter
- torchcell.adapters.ohya2005_adapter
- torchcell.adapters.ozaydin2013_adapter
- torchcell.adapters.sameith2015_adapter
- torchcell.adapters.sgd_adapter
- torchcell.adapters.smith2006_adapter
- torchcell.adapters.smith2016_adapter
- torchcell.adapters.synth_leth_db_adapter
- torchcell.adapters.vanacloig2022_adapter
- torchcell.adapters.wildenhain2015_adapter
- torchcell.adapters.xue2025_adapter
- torchcell.adapters.yoshida2012_adapter
- torchcell.adapters.zelezniak2018_adapter
- torchcell.data.aggregate
- torchcell.data.data
- torchcell.data.deduplicate
- torchcell.data.experiment_dataset
- torchcell.data.genotype_aggregate
- torchcell.data.graph_processor
- torchcell.data.mean_experiment_deduplicate
- torchcell.data.neo4j_cell
- torchcell.database.browser_style
- torchcell.database.build_command
- torchcell.database.build_dataset_lmdb
- torchcell.database.connection
- torchcell.database.tcdb
- torchcell.datamodels.compound_identity
- torchcell.datamodels.compound_identity_curate
- torchcell.datamodels.conversion
- torchcell.datamodels.fitness_composite_conversion
- torchcell.datamodels.gene_essentiality_to_fitness_conversion
- torchcell.datamodels.identity
- torchcell.datamodels.interned_constant
- torchcell.datamodels.media
- torchcell.datamodels.ontology_checks
- torchcell.datamodels.pydant
- torchcell.datamodels.schema
- torchcell.datamodels.strain_background
- torchcell.datamodels.synthetic_lethality_to_fitness_conversion
- torchcell.datamodules.cell
- torchcell.datasets.codon_frequency
- torchcell.datasets.codon_language_model
- torchcell.datasets.dataset_registry
- torchcell.datasets.esm2
- torchcell.datasets.fungal_up_down_transformer
- torchcell.datasets.node_embedding_builder
- torchcell.datasets.nucleotide_transformer
- torchcell.datasets.one_hot_gene
- torchcell.datasets.protT5
- torchcell.datasets.random_embedding
- torchcell.datasets.scerevisiae.auesukaree2009
- torchcell.datasets.scerevisiae.baryshnikova2010
- torchcell.datasets.scerevisiae.bloom2019
- torchcell.datasets.scerevisiae.cachera2023
- torchcell.datasets.scerevisiae.caudal2024
- torchcell.datasets.scerevisiae.cooper2010
- torchcell.datasets.scerevisiae.costanzo2016
- torchcell.datasets.scerevisiae.costanzo2021
- torchcell.datasets.scerevisiae.dasilveira2014
- torchcell.datasets.scerevisiae.hillenmeyer2008
- torchcell.datasets.scerevisiae.hoepfner2014
- torchcell.datasets.scerevisiae.kemmeren2014
- torchcell.datasets.scerevisiae.kuzmin2018
- torchcell.datasets.scerevisiae.kuzmin2020
- torchcell.datasets.scerevisiae.lian2019
- torchcell.datasets.scerevisiae.lopez2024
- torchcell.datasets.scerevisiae.messner2023
- torchcell.datasets.scerevisiae.mormino2022
- torchcell.datasets.scerevisiae.mota2024
- torchcell.datasets.scerevisiae.mulleder2016
- torchcell.datasets.scerevisiae.nadal_ribelles2025
- torchcell.datasets.scerevisiae.oduibhir2014
- torchcell.datasets.scerevisiae.ohnuki2018
- torchcell.datasets.scerevisiae.ohnuki2022
- torchcell.datasets.scerevisiae.ohya2005
- torchcell.datasets.scerevisiae.ozaydin2013
- torchcell.datasets.scerevisiae.sameith2015
- torchcell.datasets.scerevisiae.sgd
- torchcell.datasets.scerevisiae.smith2006
- torchcell.datasets.scerevisiae.smith2016
- torchcell.datasets.scerevisiae.synth_leth_db
- torchcell.datasets.scerevisiae.vanacloig2022
- torchcell.datasets.scerevisiae.wildenhain2015
- torchcell.datasets.scerevisiae.xue2025
- torchcell.datasets.scerevisiae.yeastphenome
- torchcell.datasets.scerevisiae.yoshida2012
- torchcell.datasets.scerevisiae.zelezniak2018
- torchcell.datasets.sgd_gene_graph
- torchcell.graph.graph
- torchcell.knowledge_graphs.build_time_projection
- torchcell.knowledge_graphs.create_kg
- torchcell.knowledge_graphs.create_scerevisiae_kg
- torchcell.knowledge_graphs.create_scerevisiae_kg_small
- torchcell.knowledge_graphs.gene_interactions_scerevisae_kg
- torchcell.knowledge_graphs.head_ontology
- torchcell.knowledge_graphs.incremental_import
- torchcell.knowledge_graphs.kg_manifest
- torchcell.knowledge_graphs.release_snapshot
- torchcell.knowledge_graphs.releases
- torchcell.knowledge_graphs.subset
- torchcell.knowledge_graphs.supported_queries.check
- torchcell.knowledge_graphs.supported_queries.cypher_deps
- torchcell.knowledge_graphs.supported_queries.registry
- torchcell.literature.backfill
- torchcell.literature.capture
- torchcell.literature.citation_keys
- torchcell.literature.manifest
- torchcell.literature.ocr
- torchcell.literature.server
- torchcell.literature.si_data
- torchcell.literature.zotero
- torchcell.loader.cpu_experiment_loader
- torchcell.loader.dense_padding_data_loader
- torchcell.losses.dango
- torchcell.losses.dcell
- torchcell.losses.diffusion_loss
- torchcell.losses.distributional
- torchcell.losses.isomorphic_cell_loss
- torchcell.losses.list_mle
- torchcell.losses.logcosh
- torchcell.losses.mle_dist_supcr
- torchcell.losses.mle_wasserstein
- torchcell.losses.multi_dim_nan_tolerant
- torchcell.losses.point_dist_graph_reg
- torchcell.metabolism.betaxanthin
- torchcell.metabolism.constraints
- torchcell.metabolism.enzyme_kinetics
- torchcell.metabolism.flux_layer
- torchcell.metabolism.media
- torchcell.metabolism.parameters
- torchcell.metabolism.pathway
- torchcell.metabolism.yeast_GEM
- torchcell.models.cell_graph_transformer
- torchcell.models.cell_graph_transformer_metabolism
- torchcell.models.dango
- torchcell.models.dcell
- torchcell.models.dcell_opt
- torchcell.models.deep_set
- torchcell.models.diffusion_decoder
- torchcell.models.equivariant_cell_graph_transformer
- torchcell.models.esm2
- torchcell.models.fungal_up_down_transformer
- torchcell.models.gpu_edge_mask_generator
- torchcell.models.hetero_cell_bipartite_dango
- torchcell.models.hetero_cell_bipartite_dango_diff_gi
- torchcell.models.hetero_cell_bipartite_dango_gi
- torchcell.models.hetero_cell_bipartite_dango_gi_lazy
- torchcell.models.hetero_cell_nsa_retry
- torchcell.models.linear
- torchcell.models.llm
- torchcell.models.mlp
- torchcell.models.nucleotide_transformer
- torchcell.models.protT5
- torchcell.models.self_attention_deep_set
- torchcell.nn.hetero_nsa
- torchcell.nn.masked_attention_block
- torchcell.nn.masked_gin_conv
- torchcell.nn.nsa_encoder
- torchcell.nn.self_attention_block
- torchcell.nn.stoichiometric_hypergraph_conv
- torchcell.ontology.tc_ontology
- torchcell.paper.ontology_graph
- torchcell.paper.ontology_svg
- torchcell.paper.signal
- torchcell.paper.tables
- torchcell.profiling.timing
- torchcell.provenance.build_manifest
- torchcell.provenance.schema_deps
- torchcell.provenance.schema_impact
- torchcell.scheduler.cosine_annealing_warmup
- torchcell.sequence.data
- torchcell.sga.assay
- torchcell.sga.cellpose_seg
- torchcell.sga.image
- torchcell.sga.io
- torchcell.sga.models
- torchcell.sga.normalize
- torchcell.sga.register
- torchcell.sga.score
- torchcell.trainers.dcell_regression
- torchcell.trainers.dcell_regression_slim
- torchcell.trainers.int_dango
- torchcell.trainers.int_dcell
- torchcell.trainers.int_hetero_cell
- torchcell.trainers.int_transformer_cell
- torchcell.trainers.neo_regression
- torchcell.trainers.simple_linear_regression
- torchcell.transforms.coo_regression_to_classification
- torchcell.transforms.hetero_to_dense_mask
- torchcell.transforms.regression_to_classification
- torchcell.utils.file_lock
- torchcell.utils.paths
- torchcell.utils.utils
- torchcell.verification.common
- torchcell.verification.expression
- torchcell.verification.fitness
- torchcell.verification.levels
- torchcell.verification.metabolite
- torchcell.verification.morphology
- torchcell.verification.report
- torchcell.verification.sourced
- torchcell.verification.visual_score
- torchcell.viz.fitness
- torchcell.viz.genetic_interaction_score
- torchcell.viz.graph_recovery
- torchcell.viz.transformer_diagnostics
- torchcell.viz.visual_graph_degen
- torchcell.viz.visual_regression