Index

_

__abstractmethods__ (decima.model.metrics.DiseaseLfcMSE attribute) (decima.model.metrics.GenePearsonCorrCoef attribute) (decima.model.metrics.WarningCounter attribute) __annotations__ (decima.core.attribution.VariantAttributionResult attribute) (decima.core.metadata.CellMetadata attribute) (decima.core.metadata.GeneMetadata attribute) (decima.core.result.DecimaResult attribute) (decima.data.dataset.HDF5Dataset attribute) (decima.data.dataset.SeqDataset attribute) (decima.data.dataset.VariantDataset attribute) (decima.model.decima_model.DecimaModel attribute) (decima.model.lightning.EnsembleLightningModel attribute) (decima.model.lightning.GeneMaskLightningModel attribute) (decima.model.lightning.LightningModel attribute) (decima.model.loss.TaskWisePoissonMultinomialLoss attribute) (decima.model.metrics.DiseaseLfcMSE attribute) (decima.model.metrics.GenePearsonCorrCoef attribute) (decima.model.metrics.WarningCounter attribute) (decima.utils.io.VariantAttributionWriter 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.core.attribution.AttributionResult method) (decima.utils.dataframe.ChunkDataFrameWriter method) (decima.utils.io.AttributionWriter method) (decima.utils.io.BigWigWriter method) (decima.utils.qc.QCLogger method) __eq__() (decima.core.metadata.CellMetadata method) (decima.core.metadata.GeneMetadata method) __exit__() (decima.core.attribution.AttributionResult method) (decima.utils.dataframe.ChunkDataFrameWriter method) (decima.utils.io.AttributionWriter method) (decima.utils.io.BigWigWriter method) (decima.utils.qc.QCLogger method) __getitem__() (decima.data.dataset.GeneDataset method) (decima.data.dataset.HDF5Dataset method) (decima.data.dataset.SeqDataset method) (decima.data.dataset.VariantDataset method) __hash__ (decima.core.metadata.CellMetadata attribute) (decima.core.metadata.GeneMetadata attribute) __init__() (decima.core.attribution.Attribution method) (decima.core.attribution.AttributionResult method) (decima.core.attribution.VariantAttributionResult method) (decima.core.metadata.CellMetadata method) (decima.core.metadata.GeneMetadata method) (decima.core.result.DecimaResult method) (decima.data.dataset.GeneDataset method) (decima.data.dataset.HDF5Dataset method) (decima.data.dataset.SeqDataset method) (decima.data.dataset.VariantDataset method) (decima.DecimaResult method) (decima.interpret.attributer.DecimaAttributer method) (decima.model.decima_model.DecimaModel method) (decima.model.lightning.EnsembleLightningModel method) (decima.model.lightning.GeneMaskLightningModel method) (decima.model.lightning.LightningModel method) (decima.model.loss.TaskWisePoissonMultinomialLoss method) (decima.model.metrics.DiseaseLfcMSE method) (decima.model.metrics.GenePearsonCorrCoef method) (decima.model.metrics.WarningCounter method) (decima.utils.dataframe.ChunkDataFrameWriter method) (decima.utils.inject.SeqBuilder method) (decima.utils.io.AttributionWriter method) (decima.utils.io.BigWigWriter method) (decima.utils.io.VariantAttributionWriter method) (decima.utils.qc.QCLogger method)

__len__() (decima.data.dataset.GeneDataset method) (decima.data.dataset.HDF5Dataset method) (decima.data.dataset.SeqDataset method) (decima.data.dataset.VariantDataset method) __match_args__ (decima.core.metadata.CellMetadata attribute) (decima.core.metadata.GeneMetadata attribute) __parameters__ (decima.data.dataset.GeneDataset attribute) (decima.data.dataset.HDF5Dataset attribute) (decima.data.dataset.SeqDataset attribute) (decima.data.dataset.VariantDataset attribute) __repr__() (decima.core.attribution.Attribution method) (decima.core.attribution.AttributionResult method) (decima.core.metadata.CellMetadata method) (decima.core.metadata.GeneMetadata method) (decima.core.result.DecimaResult method) (decima.data.dataset.VariantDataset method) (decima.DecimaResult method) __sub__() (decima.core.attribution.Attribution method)

A

add() (decima.utils.io.AttributionWriter method) (decima.utils.io.BigWigWriter method) (decima.utils.io.VariantAttributionWriter method) add_transform() (decima.model.lightning.EnsembleLightningModel method) (decima.model.lightning.LightningModel method) aggregate() (decima.core.attribution.AttributionResult static method) aggregate_anndata() (in module decima.data.preprocess) ALLELE_MISMATCH_WITH_REFERENCE_GENOME (decima.model.metrics.WarningType attribute)

assert_genes() (decima.core.result.DecimaResult method) (decima.DecimaResult method) assign_borzoi_folds() (in module decima.data.preprocess) attribute() (decima.interpret.attributer.DecimaAttributer method) Attribution (class in decima.core.attribution) AttributionResult (class in decima.core.attribution) attributions() (decima.core.result.DecimaResult method) (decima.DecimaResult method) AttributionWriter (class in decima.utils.io)

B

BigWigWriter (class in decima.utils.io)

C

cache_decima_data() (in module decima.hub.download) cache_decima_metadata() (in module decima.hub.download) cache_decima_weights() (in module decima.hub.download) cache_hg38() (in module decima.hub.download) 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.attribution.Attribution property) (decima.core.metadata.GeneMetadata attribute), [1] chunk_df() (in module decima.utils.dataframe) ChunkDataFrameWriter (class in decima.utils.dataframe) close() (decima.core.attribution.AttributionResult method) (decima.data.dataset.HDF5Dataset method) (decima.utils.io.AttributionWriter method) (decima.utils.io.BigWigWriter method) (decima.utils.io.VariantAttributionWriter method) (decima.utils.qc.QCLogger method)

co_name (decima.core.metadata.CellMetadata attribute) co_term (decima.core.metadata.CellMetadata attribute) collate_fn() (decima.data.dataset.GeneDataset method) (decima.data.dataset.SeqDataset method) (decima.data.dataset.VariantDataset method) compare_marker_zscores() (in module decima.tools.evaluate) compute() (decima.model.metrics.DiseaseLfcMSE method) (decima.model.metrics.GenePearsonCorrCoef 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) correlation() (decima.core.result.DecimaResult method) (decima.DecimaResult 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.callback module decima.cli.download module decima.cli.finetune module decima.cli.modisco module decima.cli.predict_genes module decima.cli.query_cell module decima.cli.vep module decima.cli.vep_attribution module decima.constants module decima.core module decima.core.attribution 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.write_hdf5 module decima.hub module decima.hub.download module decima.interpret module decima.interpret.attributer module decima.interpret.attributions module decima.interpret.modisco 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.inference 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.motifs module decima.utils.qc module decima.utils.sequence module decima.utils.variant module decima.vep module decima.vep.attributions module decima.vep.vep module DecimaAttributer (class in decima.interpret.attributer) 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() (in module decima.hub.download) download_decima_metadata() (in module decima.hub.download) download_decima_weights() (in module decima.hub.download) downstream_bases (decima.core.metadata.GeneMetadata attribute)

E

end (decima.core.attribution.Attribution property) (decima.core.metadata.GeneMetadata attribute), [1] ensembl_canonical_tss (decima.core.metadata.GeneMetadata attribute) ensemble_predictions() (in module decima.utils.dataframe) EnsembleLightningModel (class in decima.model.lightning)

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

frac_N (decima.core.metadata.GeneMetadata attribute), [1] frac_nan (decima.core.metadata.CellMetadata attribute) (decima.core.metadata.GeneMetadata attribute), [1] from_dataframe() (decima.data.dataset.SeqDataset class method) from_fasta() (decima.data.dataset.SeqDataset class method) from_one_hot() (decima.data.dataset.SeqDataset class method) from_seq() (decima.core.attribution.Attribution class method) from_series() (decima.core.metadata.CellMetadata class method) (decima.core.metadata.GeneMetadata class method)

G

gene_end (decima.core.attribution.Attribution property) (decima.core.metadata.GeneMetadata attribute), [1] 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.attribution.Attribution property) (decima.core.metadata.GeneMetadata attribute), [1] gene_type (decima.core.metadata.GeneMetadata attribute), [1] GeneDataset (class in decima.data.dataset) GeneMaskLightningModel (class in decima.model.lightning)

GeneMetadata (class in decima.core.metadata) GenePearsonCorrCoef (class in decima.model.metrics) genes (decima.core.result.DecimaResult property) (decima.DecimaResult property) get_attribution_method() (in module decima.interpret.attributer) 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) ground_truth (decima.core.result.DecimaResult property) (decima.DecimaResult property)

H

HDF5Dataset (class in decima.data.dataset)

higher_is_better (decima.model.metrics.WarningCounter attribute)

I

import_cyvcf2() (in module decima.utils.io) import_plotnine() (in module decima.plot.visualize)

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.attribution.AttributionResult method) (decima.core.attribution.VariantAttributionResult method) (decima.core.result.DecimaResult class method) (decima.DecimaResult class method) load_attribution() (decima.core.attribution.AttributionResult method) (decima.core.attribution.VariantAttributionResult method) load_decima_attributer() (decima.interpret.attributer.DecimaAttributer class method) load_decima_metadata() (in module decima.hub)

load_decima_model() (in module decima.hub) load_from_checkpoints() (decima.model.lightning.EnsembleLightningModel class method) load_model() (decima.core.result.DecimaResult method) (decima.DecimaResult method) load_ncbi_string() (in module decima.data.preprocess) load_safetensor() (decima.model.lightning.LightningModel class method) log() (decima.utils.qc.QCLogger method) log_correlation() (decima.utils.qc.QCLogger method) log_gene() (decima.utils.qc.QCLogger method) 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() (decima.core.result.DecimaResult method) (decima.DecimaResult method) (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) max_counts (decima.core.metadata.GeneMetadata attribute) mean_counts (decima.core.metadata.GeneMetadata attribute), [1] merge_transcripts() (in module decima.data.preprocess) model (decima.core.result.DecimaResult property) (decima.DecimaResult property) modisco() (in module decima.interpret.modisco) modisco_patterns() (in module decima.interpret.modisco) modisco_reports() (in module decima.interpret.modisco) modisco_seqlet_bed() (in module decima.interpret.modisco) module decima decima.cli decima.cli.attributions decima.cli.callback decima.cli.download decima.cli.finetune decima.cli.modisco decima.cli.predict_genes decima.cli.query_cell decima.cli.vep decima.cli.vep_attribution decima.constants decima.core decima.core.attribution decima.core.metadata decima.core.result decima.data decima.data.dataset decima.data.preprocess decima.data.read_hdf5 decima.data.write_hdf5 decima.hub decima.hub.download decima.interpret decima.interpret.attributer decima.interpret.attributions decima.interpret.modisco 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.inference decima.tools.interpret decima.train decima.utils decima.utils.dataframe decima.utils.inject decima.utils.io decima.utils.motifs decima.utils.qc decima.utils.sequence decima.utils.variant decima.vep decima.vep.attributions decima.vep.vep

motif_start_end() (in module decima.utils.motifs) 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) one_hot_to_seq() (in module decima.utils.sequence) open() (decima.core.attribution.AttributionResult method) (decima.core.attribution.VariantAttributionResult method) (decima.utils.io.AttributionWriter method) (decima.utils.io.BigWigWriter method) (decima.utils.io.VariantAttributionWriter method) (decima.utils.qc.QCLogger method)

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

P

parse_attributions() (in module decima.cli.callback) parse_genes() (in module decima.cli.callback) parse_logger() (decima.model.lightning.LightningModel method) parse_metadata() (in module decima.cli.callback) parse_model() (in module decima.cli.callback) peaks (decima.core.attribution.Attribution property) peaks_to_bed() (decima.core.attribution.Attribution method) pearson (decima.core.metadata.GeneMetadata attribute), [1] plot_attributions() (in module decima.interpret.attributions) plot_correlation() (decima.core.result.DecimaResult method) (decima.DecimaResult method) plot_gene_scatter() (in module decima.plot.visualize) plot_marker_box() (in module decima.plot.visualize) plot_peaks() (decima.core.attribution.Attribution method) (in module decima.plot.visualize) plot_seqlogo() (decima.core.attribution.Attribution method) plot_track_scatter() (in module decima.plot.visualize) predict_attributions_seqlet_calling() (in module decima) (in module decima.interpret.attributions)

predict_gene_expression() (in module decima.tools.inference) predict_on_dataset() (decima.model.lightning.EnsembleLightningModel method) (decima.model.lightning.LightningModel method) predict_save_attributions() (in module decima.interpret.attributions) predict_save_modisco_attributions() (in module decima.interpret.modisco) predict_step() (decima.model.lightning.EnsembleLightningModel method) (decima.model.lightning.LightningModel method) predict_variant_effect() (in module decima) (in module decima.vep) (in module decima.vep.vep) predicted_expression_cache() (decima.data.dataset.VariantDataset method) predicted_expression_matrix() (decima.core.result.DecimaResult method) (decima.DecimaResult method) predicted_gene_expression() (decima.core.result.DecimaResult method) (decima.DecimaResult method) prepare_mask_gene() (in module decima.utils.sequence) 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

QCLogger (class in decima.utils.qc) 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_metadata_from_replicate_parquets() (in module decima.utils.dataframe) read_vcf_chunks() (in module decima.utils.io) recursive_seqlet_calling() (decima.core.attribution.AttributionResult method) (decima.core.attribution.VariantAttributionResult method) (in module decima.interpret.attributions)

region (decima.core.metadata.CellMetadata attribute), [1] reset() (decima.model.metrics.DiseaseLfcMSE method) (decima.model.metrics.GenePearsonCorrCoef method) reset_transform() (decima.model.lightning.EnsembleLightningModel method) (decima.model.lightning.LightningModel method) return_ensembl() (in module decima.data.preprocess)

S

save_bigwig() (decima.core.attribution.Attribution method) save_fasta() (decima.core.attribution.Attribution method) save_peaks() (decima.core.attribution.Attribution method) scan_attributions() (in module decima.tools.interpret) scan_motifs() (decima.core.attribution.Attribution method) SeqBuilder (class in decima.utils.inject) SeqDataset (class in decima.data.dataset) 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.attribution.Attribution property) (decima.core.metadata.GeneMetadata attribute), [1] strand (decima.core.attribution.Attribution property) (decima.core.metadata.GeneMetadata attribute), [1] 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.EnsembleLightningModel method) (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.EnsembleLightningModel method) (decima.model.lightning.LightningModel method) transform() (decima.model.lightning.EnsembleLightningModel method)

U

UNKNOWN (decima.model.metrics.WarningType attribute) update() (decima.model.metrics.DiseaseLfcMSE method) (decima.model.metrics.GenePearsonCorrCoef method) (decima.model.metrics.WarningCounter method)

upstream_bases (decima.core.metadata.GeneMetadata attribute)

V

val_pearson (decima.core.metadata.CellMetadata attribute), [1] validate_allele_seq() (decima.data.dataset.VariantDataset method) validate_save_replicates() (in module decima.cli.callback) validation_step() (decima.model.lightning.EnsembleLightningModel method) (decima.model.lightning.LightningModel method)

var_to_intervals() (in module decima.data.preprocess) variant_effect_attribution() (in module decima.vep) (in module decima.vep.attributions) VariantAttributionResult (class in decima.core.attribution) VariantAttributionWriter (class in decima.utils.io) 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)