Index

_

__abstractmethods__ (decima.model.metrics.DiseaseLfcMSE attribute) (decima.model.metrics.WarningCounter attribute) __annotations__ (decima.core.metadata.CellMetadata attribute) (decima.core.metadata.GeneMetadata attribute) (decima.core.result.DecimaResult attribute) (decima.data.dataset.VariantDataset attribute) (decima.model.decima_model.DecimaModel attribute) (decima.model.lightning.LightningModel attribute) (decima.model.loss.TaskWisePoissonMultinomialLoss attribute) (decima.model.metrics.DiseaseLfcMSE attribute) (decima.model.metrics.WarningCounter attribute) __dataclass_fields__ (decima.core.metadata.CellMetadata attribute) (decima.core.metadata.GeneMetadata attribute) __dataclass_params__ (decima.core.metadata.CellMetadata attribute) (decima.core.metadata.GeneMetadata attribute) __enter__() (decima.utils.dataframe.ChunkDataFrameWriter method) __eq__() (decima.core.metadata.CellMetadata method) (decima.core.metadata.GeneMetadata method) __exit__() (decima.utils.dataframe.ChunkDataFrameWriter method) __getitem__() (decima.data.dataset.HDF5Dataset method) (decima.data.dataset.VariantDataset method) __hash__ (decima.core.metadata.CellMetadata attribute) (decima.core.metadata.GeneMetadata attribute) __init__() (decima.core.metadata.CellMetadata method) (decima.core.metadata.GeneMetadata method) (decima.core.result.DecimaResult method) (decima.data.dataset.HDF5Dataset method) (decima.data.dataset.VariantDataset method) (decima.DecimaResult method) (decima.interpret.attributions.Attribution method) (decima.model.decima_model.DecimaModel method) (decima.model.lightning.LightningModel method) (decima.model.loss.TaskWisePoissonMultinomialLoss method) (decima.model.metrics.DiseaseLfcMSE method) (decima.model.metrics.WarningCounter method) (decima.utils.dataframe.ChunkDataFrameWriter method) (decima.utils.inject.SeqBuilder method)

__len__() (decima.data.dataset.HDF5Dataset method) (decima.data.dataset.VariantDataset method) __match_args__ (decima.core.metadata.CellMetadata attribute) (decima.core.metadata.GeneMetadata attribute) __parameters__ (decima.data.dataset.HDF5Dataset attribute) (decima.data.dataset.VariantDataset attribute) __repr__() (decima.core.metadata.CellMetadata method) (decima.core.metadata.GeneMetadata method) (decima.core.result.DecimaResult method) (decima.DecimaResult method) (decima.interpret.attributions.Attribution method)

A

add_transform() (decima.model.lightning.LightningModel method) aggregate_anndata() (in module decima.data.preprocess) ALLELE_MISMATCH_WITH_REFERENCE_GENOME (decima.model.metrics.WarningType attribute) assign_borzoi_folds() (in module decima.data.preprocess)

Attribution (class in decima.interpret.attributions) attributions() (decima.core.result.DecimaResult method) (decima.DecimaResult method) (in module decima.interpret.attributions)

C

cell_metadata (decima.core.result.DecimaResult property) (decima.DecimaResult property) cell_type (decima.core.metadata.CellMetadata attribute), [1] CellMetadata (class in decima.core.metadata) cells (decima.core.result.DecimaResult property) (decima.DecimaResult property) celltype_coarse (decima.core.metadata.CellMetadata attribute), [1] change_values() (in module decima.data.preprocess) chrom (decima.core.metadata.GeneMetadata attribute), [1] (decima.interpret.attributions.Attribution property) chunk_df() (in module decima.utils.dataframe)

ChunkDataFrameWriter (class in decima.utils.dataframe) close() (decima.data.dataset.HDF5Dataset method) collate_fn() (decima.data.dataset.VariantDataset method) compare_marker_zscores() (in module decima.tools.evaluate) compute() (decima.model.metrics.DiseaseLfcMSE method) (decima.model.metrics.WarningCounter method) compute_marker_metrics() (in module decima.tools.evaluate) concat() (decima.utils.inject.SeqBuilder method) configure_optimizers() (decima.model.lightning.LightningModel method) count_genes() (in module decima.data.read_hdf5) count_params() (decima.model.lightning.LightningModel method)

D

dataset (decima.core.metadata.CellMetadata attribute), [1] (decima.core.metadata.GeneMetadata attribute), [1] decima module decima.cli module decima.cli.attributions module decima.cli.download module decima.cli.finetune module decima.cli.predict_genes module decima.cli.query_cell module decima.cli.vep module decima.constants module decima.core module decima.core.metadata module decima.core.result module decima.data module decima.data.dataset module decima.data.preprocess module decima.data.read_hdf5 module decima.data.read_vcf module decima.data.write_hdf5 module decima.dataloaders module decima.hub module decima.hub.download module decima.interpret module decima.interpret.attributions module

decima.interpret.ism module decima.interpret.save_attributions module decima.model module decima.model.decima_model module decima.model.lightning module decima.model.loss module decima.model.metrics module decima.plot module decima.plot.visualize module decima.tools module decima.tools.evaluate module decima.tools.interpret module decima.train module decima.utils module decima.utils.dataframe module decima.utils.inject module decima.utils.io module decima.utils.variant module decima.vep module DecimaModel (class in decima.model.decima_model) DecimaResult (class in decima) (class in decima.core.result) DEFAULT_COLUMNS (decima.data.dataset.VariantDataset attribute) disease (decima.core.metadata.CellMetadata attribute), [1] DiseaseLfcMSE (class in decima.model.metrics) download_decima_data() (in module decima.hub.download) download_decima_metadata() (in module decima.hub.download) download_decima_weights() (in module decima.hub.download) download_hg38() (in module decima.hub.download)

E

end (decima.core.metadata.GeneMetadata attribute), [1] (decima.interpret.attributions.Attribution property) extract_gene_data() (in module decima.data.read_hdf5)

extract_label() (decima.data.dataset.HDF5Dataset method) extract_seq() (decima.data.dataset.HDF5Dataset method) extract_tasks() (decima.data.dataset.HDF5Dataset method)

F

fasta_str() (decima.interpret.attributions.Attribution method) find_attr_peaks() (in module decima.tools.interpret) find_peaks() (decima.interpret.attributions.Attribution static method) fold (decima.core.metadata.GeneMetadata attribute), [1] format_input() (decima.model.lightning.LightningModel method) forward() (decima.model.lightning.LightningModel method) (decima.model.loss.TaskWisePoissonMultinomialLoss method)

frac_N (decima.core.metadata.GeneMetadata attribute), [1] frac_nan (decima.core.metadata.GeneMetadata attribute), [1] from_seq() (decima.interpret.attributions.Attribution class method) from_series() (decima.core.metadata.CellMetadata class method) (decima.core.metadata.GeneMetadata class method)

G

gene_end (decima.core.metadata.GeneMetadata attribute), [1] (decima.interpret.attributions.Attribution property) gene_id (decima.core.metadata.GeneMetadata attribute), [1] gene_length (decima.core.metadata.GeneMetadata attribute), [1] gene_mask_end (decima.core.metadata.GeneMetadata attribute), [1] gene_mask_start (decima.core.metadata.GeneMetadata attribute), [1] gene_metadata (decima.core.result.DecimaResult property) (decima.DecimaResult property) gene_sequence() (decima.core.result.DecimaResult method) (decima.DecimaResult method) gene_start (decima.core.metadata.GeneMetadata attribute), [1] (decima.interpret.attributions.Attribution property)

gene_type (decima.core.metadata.GeneMetadata attribute), [1] GeneMetadata (class in decima.core.metadata) genes (decima.core.result.DecimaResult property) (decima.DecimaResult property) get_attribution_method() (in module decima.interpret.attributions) get_cell_metadata() (decima.core.result.DecimaResult method) (decima.DecimaResult method) get_compute_device() (in module decima.utils) get_frac_N() (in module decima.data.preprocess) get_gene_idx() (in module decima.data.read_hdf5) get_gene_metadata() (decima.core.result.DecimaResult method) (decima.DecimaResult method) get_task_idxs() (decima.model.lightning.LightningModel method)

H

HDF5Dataset (class in decima.data.dataset)

higher_is_better (decima.model.metrics.WarningCounter attribute)

I

index_genes() (in module decima.data.read_hdf5)

inject() (decima.utils.inject.SeqBuilder method) is_differentiable (decima.model.metrics.WarningCounter attribute)

L

LightningModel (class in decima.model.lightning) list_genes() (in module decima.data.read_hdf5) load() (decima.core.result.DecimaResult class method) (decima.DecimaResult class method) load_decima_metadata() (in module decima.hub)

load_decima_model() (in module decima.hub) load_model() (decima.core.result.DecimaResult method) (decima.DecimaResult method) load_ncbi_string() (in module decima.data.preprocess) login_wandb() (in module decima.hub)

M

make_inputs() (in module decima.data.preprocess) make_predict_loader() (decima.model.lightning.LightningModel method) make_test_loader() (decima.model.lightning.LightningModel method) make_train_loader() (decima.model.lightning.LightningModel method) marker_zscores() (in module decima.tools.evaluate) match_cellranger_2024() (in module decima.data.preprocess) match_criteria() (in module decima.tools.evaluate) match_ncbi() (in module decima.data.preprocess) match_ref_ad() (in module decima.data.preprocess) mean_counts (decima.core.metadata.GeneMetadata attribute), [1] merge_transcripts() (in module decima.data.preprocess) model (decima.core.result.DecimaResult property) (decima.DecimaResult property) module decima decima.cli decima.cli.attributions decima.cli.download decima.cli.finetune decima.cli.predict_genes decima.cli.query_cell decima.cli.vep decima.constants decima.core decima.core.metadata decima.core.result decima.data decima.data.dataset decima.data.preprocess decima.data.read_hdf5 decima.data.read_vcf decima.data.write_hdf5 decima.dataloaders decima.hub decima.hub.download decima.interpret decima.interpret.attributions decima.interpret.ism decima.interpret.save_attributions decima.model decima.model.decima_model decima.model.lightning decima.model.loss decima.model.metrics decima.plot decima.plot.visualize decima.tools decima.tools.evaluate decima.tools.interpret decima.train decima.utils decima.utils.dataframe decima.utils.inject decima.utils.io decima.utils.variant decima.vep

mutate() (in module decima.data.read_hdf5)

N

n_cells (decima.core.metadata.CellMetadata attribute), [1] n_genes (decima.core.metadata.CellMetadata attribute), [1]

n_tracks (decima.core.metadata.GeneMetadata attribute), [1] name (decima.core.metadata.CellMetadata attribute), [1] (decima.core.metadata.GeneMetadata attribute), [1]

O

on_save_checkpoint() (decima.model.lightning.LightningModel method) on_test_epoch_end() (decima.model.lightning.LightningModel method)

on_validation_epoch_end() (decima.model.lightning.LightningModel method) organ (decima.core.metadata.CellMetadata attribute), [1] overlap_genes() (decima.data.dataset.VariantDataset static method)

P

parse_logger() (decima.model.lightning.LightningModel method) peaks_to_bed() (decima.interpret.attributions.Attribution method) pearson (decima.core.metadata.GeneMetadata attribute), [1] plot_gene_scatter() (in module decima.plot.visualize) plot_marker_box() (in module decima.plot.visualize) plot_peaks() (decima.interpret.attributions.Attribution method) (in module decima.plot.visualize) plot_seqlogo() (decima.interpret.attributions.Attribution method) plot_track_scatter() (in module decima.plot.visualize) predict_on_dataset() (decima.model.lightning.LightningModel method)

predict_save_attributions() (in module decima) (in module decima.interpret.save_attributions) predict_step() (decima.model.lightning.LightningModel method) predict_variant_effect() (in module decima) (in module decima.vep) predicted_expression_matrix() (decima.core.result.DecimaResult method) (decima.DecimaResult method) prepare_one_hot() (decima.core.result.DecimaResult method) (decima.DecimaResult method) prepare_seq_alt_allele() (in module decima.utils.inject) process_variants() (in module decima.utils.variant)

Q

query_cells() (decima.core.result.DecimaResult method) (decima.DecimaResult method)

query_tasks() (decima.core.result.DecimaResult method) (decima.DecimaResult method)

R

read_fasta_gene_mask() (in module decima.utils.io) read_vcf_chunks() (in module decima.utils.io)

region (decima.core.metadata.CellMetadata attribute), [1] reset() (decima.model.metrics.DiseaseLfcMSE method) reset_transform() (decima.model.lightning.LightningModel method)

S

save_bigwig() (decima.interpret.attributions.Attribution method) save_fasta() (decima.interpret.attributions.Attribution method) save_peaks() (decima.interpret.attributions.Attribution method) scan_attributions() (in module decima.tools.interpret) scan_motifs() (decima.interpret.attributions.Attribution method) SeqBuilder (class in decima.utils.inject) shape (decima.core.result.DecimaResult property) (decima.DecimaResult property)

size_factor (decima.core.metadata.CellMetadata attribute), [1] size_factor_pearson (decima.core.metadata.GeneMetadata attribute), [1] start (decima.core.metadata.GeneMetadata attribute), [1] (decima.interpret.attributions.Attribution property) strand (decima.core.metadata.GeneMetadata attribute), [1] (decima.interpret.attributions.Attribution property) study (decima.core.metadata.CellMetadata attribute), [1] subregion (decima.core.metadata.CellMetadata attribute), [1]

T

TaskWisePoissonMultinomialLoss (class in decima.model.loss) test_pearson (decima.core.metadata.CellMetadata attribute), [1] test_step() (decima.model.lightning.LightningModel method) tissue (decima.core.metadata.CellMetadata attribute), [1]

total_counts (decima.core.metadata.CellMetadata attribute), [1] train_on_dataset() (decima.model.lightning.LightningModel method) train_pearson (decima.core.metadata.CellMetadata attribute), [1] training_step() (decima.model.lightning.LightningModel method)

U

UNKNOWN (decima.model.metrics.WarningType attribute)

update() (decima.model.metrics.DiseaseLfcMSE method) (decima.model.metrics.WarningCounter method)

V

val_pearson (decima.core.metadata.CellMetadata attribute), [1] validate_allele_seq() (decima.data.dataset.VariantDataset method)

validation_step() (decima.model.lightning.LightningModel method) var_to_intervals() (in module decima.data.preprocess) VariantDataset (class in decima.data.dataset)

W

WarningCounter (class in decima.model.metrics) WarningType (class in decima.model.metrics)

write() (decima.utils.dataframe.ChunkDataFrameWriter method) write_df_chunks_to_parquet() (in module decima.utils.dataframe) write_hdf5() (in module decima.data.write_hdf5)