Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X A AbstractAnnotation (class in alphagenome.visualization.plot_components) AbstractComponent (class in alphagenome.visualization.plot_components) acceptor (alphagenome.data.genome.Junction attribute) acceptor_region() (alphagenome.data.genome.Junction method) ACTIVE_MEAN (alphagenome.models.v1.variant_scorers.AggregationType attribute) (alphagenome.models.v2.variant_scorers.AggregationType attribute) ACTIVE_SUM (alphagenome.models.v1.variant_scorers.AggregationType attribute) (alphagenome.models.v2.variant_scorers.AggregationType attribute) add_label() (alphagenome.visualization.plot_components.AbstractAnnotation method) (alphagenome.visualization.plot_components.IntervalAnnotation method) (alphagenome.visualization.plot_components.VariantAnnotation method) aggregation_type (alphagenome.models.v1.interval_scorers.GeneMaskScorer attribute) (alphagenome.models.v1.variant_scorers.CenterMaskScorer attribute) (alphagenome.models.v2.interval_scorers.GeneMaskScorer attribute) (alphagenome.models.v2.variant_scorers.CenterMaskScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskLFCScorer attribute) AggregationType (class in alphagenome.data.track_data) (class in alphagenome.models.v1.variant_scorers) (class in alphagenome.models.v2.variant_scorers) ALL_FOLDS (alphagenome.models.v1.dna_client.ModelVersion attribute) (alphagenome.models.v2.dna_client.ModelVersion attribute) alphagenome.atlas module alphagenome.interpretation module alphagenome.models.v1.interval_scorers.IntervalScorerTypes (in module alphagenome) alphagenome.models.v2.interval_scorers.IntervalScorerTypes (in module alphagenome) alternate (alphagenome.models.v1.dna_output.VariantOutput attribute) (alphagenome.models.v2.dna_output.VariantOutput attribute) alternate_bases (alphagenome.data.genome.Variant attribute) alternate_overlaps() (alphagenome.data.genome.Variant method) annotations (alphagenome.visualization.plot_components.AbstractAnnotation attribute) ARTIFACT (alphagenome.data.gene_annotation.TranscriptType attribute) as_truncated_str() (alphagenome.data.genome.Variant method) as_unstranded() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) assign_consensus_enhancers() (in module alphagenome.interpretation.enhancer_scoring) atac (alphagenome.models.v1.dna_output.Output attribute) (alphagenome.models.v1.dna_output.OutputMetadata attribute) ATAC (alphagenome.models.v1.dna_output.OutputType attribute) atac (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) ATAC (alphagenome.models.v2.dna_output.OutputType attribute) AtlasClient (class in alphagenome.atlas.atlas) B base_interval_scorer (alphagenome.models.v1.interval_scorers.GeneMaskScorer attribute) (alphagenome.models.v2.interval_scorers.GeneMaskScorer attribute) base_variant_scorer (alphagenome.models.v1.variant_scorers.CenterMaskScorer attribute) (alphagenome.models.v1.variant_scorers.ContactMapScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskActiveScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskLFCScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskSplicingScorer attribute) (alphagenome.models.v1.variant_scorers.PolyadenylationScorer attribute) (alphagenome.models.v1.variant_scorers.SpliceJunctionScorer attribute) (alphagenome.models.v2.variant_scorers.CenterMaskScorer attribute) (alphagenome.models.v2.variant_scorers.ContactMapScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskActiveScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskLFCScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskSplicingScorer attribute) (alphagenome.models.v2.variant_scorers.MethylationScorer attribute) (alphagenome.models.v2.variant_scorers.PolyadenylationScorer attribute) (alphagenome.models.v2.variant_scorers.SpliceJunctionScorer attribute) BaseIntervalScorer (class in alphagenome.models.v1.interval_scorers) (class in alphagenome.models.v2.interval_scorers) BaseVariantScorer (class in alphagenome.models.v1.variant_scorers) (class in alphagenome.models.v2.variant_scorers) bin_index() (alphagenome.data.track_data.TrackData method) binary_mask() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) binary_mask_stranded() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) biosample_name (alphagenome.models.v2.dna_output.InputGradientsOutput attribute) boundary_shift() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) C cache_transcripts() (alphagenome.data.transcript.TranscriptExtractor method) cage (alphagenome.models.v1.dna_output.Output attribute) (alphagenome.models.v1.dna_output.OutputMetadata attribute) CAGE (alphagenome.models.v1.dna_output.OutputType attribute) cage (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) CAGE (alphagenome.models.v2.dna_output.OutputType attribute) cds (alphagenome.data.transcript.Transcript attribute) cds_color (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute) cds_height (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute) cds_including_stop_codon (alphagenome.data.transcript.Transcript attribute) cell_embeddings (alphagenome.models.v2.dna_output.Output attribute) CELL_EMBEDDINGS (alphagenome.models.v2.dna_output.OutputType attribute) center() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) CENTER_MASK (alphagenome.models.v1.variant_scorers.BaseVariantScorer attribute) (alphagenome.models.v2.variant_scorers.BaseVariantScorer attribute) CenterMaskScorer (class in alphagenome.models.v1.variant_scorers) (class in alphagenome.models.v2.variant_scorers) change_resolution() (alphagenome.data.track_data.TrackData method) channel (alphagenome.models.v1.dna_client.DnaClient attribute) (alphagenome.models.v2.dna_client.DnaClient attribute) chip_histone (alphagenome.models.v1.dna_output.Output attribute) (alphagenome.models.v1.dna_output.OutputMetadata attribute) CHIP_HISTONE (alphagenome.models.v1.dna_output.OutputType attribute) chip_histone (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) CHIP_HISTONE (alphagenome.models.v2.dna_output.OutputType attribute) chip_tf (alphagenome.models.v1.dna_output.Output attribute) (alphagenome.models.v1.dna_output.OutputMetadata attribute) CHIP_TF (alphagenome.models.v1.dna_output.OutputType attribute) chip_tf (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) CHIP_TF (alphagenome.models.v2.dna_output.OutputType attribute) chromosome (alphagenome.data.genome.Interval attribute) (alphagenome.data.genome.Junction attribute) (alphagenome.data.genome.Variant attribute) (alphagenome.data.transcript.Transcript attribute) cl (alphagenome.models.v2.model_condition.ModelCondition attribute) clo (alphagenome.models.v2.model_condition.ModelCondition attribute) colors (alphagenome.visualization.plot_components.AbstractAnnotation attribute) concat() (in module alphagenome.data.gene_expression_data) (in module alphagenome.data.track_data) concatenate() (alphagenome.models.v1.dna_output.OutputMetadata method) (alphagenome.models.v2.dna_output.OutputMetadata method) CONTACT_MAP (alphagenome.models.v1.variant_scorers.BaseVariantScorer attribute) (alphagenome.models.v2.variant_scorers.BaseVariantScorer attribute) contact_maps (alphagenome.models.v1.dna_output.Output attribute) (alphagenome.models.v1.dna_output.OutputMetadata attribute) CONTACT_MAPS (alphagenome.models.v1.dna_output.OutputType attribute) contact_maps (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) CONTACT_MAPS (alphagenome.models.v2.dna_output.OutputType attribute) ContactMaps (class in alphagenome.visualization.plot_components) ContactMapScorer (class in alphagenome.models.v1.variant_scorers) (class in alphagenome.models.v2.variant_scorers) ContactMapsDiff (class in alphagenome.visualization.plot_components) contains() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) copy() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) (alphagenome.data.genome.Variant method) (alphagenome.data.track_data.TrackData method) coverage() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) coverage_stranded() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) create() (in module alphagenome.atlas.atlas) (in module alphagenome.models.v1.dna_client) (in module alphagenome.models.v2.dna_client) D DEFAULT_GRADIENT_SCORE_THRESHOLDS (in module alphagenome.interpretation.enhancer_scoring) DIFF_LOG2_SUM (alphagenome.models.v1.variant_scorers.AggregationType attribute) (alphagenome.models.v2.variant_scorers.AggregationType attribute) DIFF_MEAN (alphagenome.models.v1.variant_scorers.AggregationType attribute) (alphagenome.models.v2.variant_scorers.AggregationType attribute) DIFF_SUM (alphagenome.models.v1.variant_scorers.AggregationType attribute) (alphagenome.models.v2.variant_scorers.AggregationType attribute) DIFF_SUM_LOG2 (alphagenome.models.v1.variant_scorers.AggregationType attribute) (alphagenome.models.v2.variant_scorers.AggregationType attribute) dinucleotide_region() (alphagenome.data.genome.Junction method) DnaClient (class in alphagenome.models.v1.dna_client) (class in alphagenome.models.v2.dna_client) dnase (alphagenome.models.v1.dna_output.Output attribute) (alphagenome.models.v1.dna_output.OutputMetadata attribute) DNASE (alphagenome.models.v1.dna_output.OutputType attribute) dnase (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) DNASE (alphagenome.models.v2.dna_output.OutputType attribute) donor (alphagenome.data.genome.Junction attribute) donor_region() (alphagenome.data.genome.Junction method) downsample() (alphagenome.data.track_data.TrackData method) draw_interval() (in module alphagenome.visualization.plot_transcripts) draw_transcript() (in module alphagenome.visualization.plot_transcripts) E efo (alphagenome.models.v2.model_condition.ModelCondition attribute) EmptyComponent (class in alphagenome.visualization.plot_components) encode_cells() (alphagenome.models.v2.dna_client.DnaClient method) end (alphagenome.data.genome.Interval attribute) (alphagenome.data.genome.Junction attribute) (alphagenome.data.genome.Variant attribute) enhancer_arcs_plot() (in module alphagenome.visualization.plot) EnhancerArcs (class in alphagenome.visualization.plot_components) exons (alphagenome.data.transcript.Transcript attribute) extract() (alphagenome.data.transcript.TranscriptExtractor method) (alphagenome.io.fasta.FastaExtractor method) extract_tss() (in module alphagenome.data.gene_annotation) F FastaExtractor (class in alphagenome.io.fasta) FeatureContribution (class in alphagenome.visualization.plot_components) filter_by_name() (alphagenome.data.junction_data.JunctionData method) filter_by_ontology() (alphagenome.data.junction_data.JunctionData method) filter_by_tissue() (alphagenome.data.junction_data.JunctionData method) filter_ontology_terms() (alphagenome.models.v1.dna_output.Output method) filter_output_type() (alphagenome.models.v1.dna_output.Output method) (alphagenome.models.v2.dna_output.Output method) filter_protein_coding() (in module alphagenome.data.gene_annotation) filter_to_longest_transcript() (in module alphagenome.data.gene_annotation) filter_to_mane_select_transcript() (in module alphagenome.data.gene_annotation) filter_to_negative_strand() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.junction_data.JunctionData method) (alphagenome.data.track_data.TrackData method) filter_to_nonnegative_strand() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.track_data.TrackData method) filter_to_nonpositive_strand() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.track_data.TrackData method) filter_to_observed() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.junction_data.JunctionData method) (alphagenome.data.track_data.TrackData method) (alphagenome.models.v2.dna_output.Output method) filter_to_positive_strand() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.junction_data.JunctionData method) (alphagenome.data.track_data.TrackData method) filter_to_protein_coding() (alphagenome.data.gene_expression_data.GeneExpressionData method) filter_to_strand() (alphagenome.data.junction_data.JunctionData method) (alphagenome.models.v1.dna_output.Output method) (alphagenome.models.v2.dna_output.Output method) filter_to_stranded() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.track_data.TrackData method) filter_to_unstranded() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.track_data.TrackData method) filter_tracks() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.junction_data.JunctionData method) (alphagenome.data.track_data.TrackData method) filter_transcript_support_level() (in module alphagenome.data.gene_annotation) filter_transcript_type() (in module alphagenome.data.gene_annotation) first_noncoding_exon_color (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute) fix_truncation() (alphagenome.data.transcript.Transcript class method) FOLD_0 (alphagenome.models.v1.dna_client.ModelVersion attribute) FOLD_1 (alphagenome.models.v1.dna_client.ModelVersion attribute) (alphagenome.models.v2.dna_client.ModelVersion attribute) FOLD_2 (alphagenome.models.v1.dna_client.ModelVersion attribute) FOLD_3 (alphagenome.models.v1.dna_client.ModelVersion attribute) from_anndata() (in module alphagenome.models.v2.gene_counts_condition) from_curie() (in module alphagenome.data.ontology) from_curies() (in module alphagenome.data.ontology) (in module alphagenome.models.v2.model_condition) from_dict() (alphagenome.data.genome.Variant class method) from_gtf_df() (alphagenome.data.transcript.Transcript class method) from_interval_dict() (alphagenome.data.genome.Interval class method) (alphagenome.data.genome.Junction class method) from_outputs() (alphagenome.models.v1.dna_output.OutputMetadata class method) from_str() (alphagenome.data.genome.Interval class method) (alphagenome.data.genome.Junction class method) (alphagenome.data.genome.Strand class method) (alphagenome.data.genome.Variant class method) G gene_id (alphagenome.data.transcript.Transcript attribute) (alphagenome.models.v2.dna_output.InputGradientsOutput attribute) (alphagenome.models.v2.dna_output.TargetGeneMetadata attribute) GENE_MASK (alphagenome.models.v1.interval_scorers.BaseIntervalScorer attribute) (alphagenome.models.v2.interval_scorers.BaseIntervalScorer attribute) GENE_MASK_ACTIVE (alphagenome.models.v1.variant_scorers.BaseVariantScorer attribute) (alphagenome.models.v2.variant_scorers.BaseVariantScorer attribute) GENE_MASK_LFC (alphagenome.models.v1.variant_scorers.BaseVariantScorer attribute) (alphagenome.models.v2.variant_scorers.BaseVariantScorer attribute) GENE_MASK_SPLICING (alphagenome.models.v1.variant_scorers.BaseVariantScorer attribute) (alphagenome.models.v2.variant_scorers.BaseVariantScorer attribute) gene_metadata (alphagenome.data.gene_expression_data.GeneExpressionData attribute) gene_name (alphagenome.models.v2.dna_output.InputGradientsOutput attribute) (alphagenome.models.v2.dna_output.TargetGeneMetadata attribute) gene_type (alphagenome.models.v2.dna_output.TargetGeneMetadata attribute) GeneExpression (class in alphagenome.visualization.plot_components) GeneExpressionData (class in alphagenome.data.gene_expression_data) GeneMaskActiveScorer (class in alphagenome.models.v1.variant_scorers) (class in alphagenome.models.v2.variant_scorers) GeneMaskLFCScorer (class in alphagenome.models.v1.variant_scorers) (class in alphagenome.models.v2.variant_scorers) GeneMaskScorer (class in alphagenome.models.v1.interval_scorers) (class in alphagenome.models.v2.interval_scorers) GeneMaskSplicingScorer (class in alphagenome.models.v1.variant_scorers) (class in alphagenome.models.v2.variant_scorers) get() (alphagenome.models.v1.dna_output.Output method) (alphagenome.models.v1.dna_output.OutputMetadata method) (alphagenome.models.v2.dna_output.Output method) (alphagenome.models.v2.dna_output.OutputMetadata method) get_active_enhancers() (in module alphagenome.interpretation.enhancer_scoring) get_all_folds() (in module alphagenome.data.fold_intervals) get_api_key() (in module alphagenome.colab_utils) get_ax_height() (alphagenome.visualization.plot_components.AbstractComponent method) (alphagenome.visualization.plot_components.ContactMaps method) (alphagenome.visualization.plot_components.ContactMapsDiff method) (alphagenome.visualization.plot_components.EmptyComponent method) (alphagenome.visualization.plot_components.EnhancerArcs method) (alphagenome.visualization.plot_components.FeatureContribution method) (alphagenome.visualization.plot_components.GeneExpression method) (alphagenome.visualization.plot_components.OverlaidGeneExpression method) (alphagenome.visualization.plot_components.OverlaidTracks method) (alphagenome.visualization.plot_components.Sashimi method) (alphagenome.visualization.plot_components.ScoreBar method) (alphagenome.visualization.plot_components.SeqLogo method) (alphagenome.visualization.plot_components.Tracks method) (alphagenome.visualization.plot_components.TranscriptAnnotation method) get_fold_intervals() (in module alphagenome.data.fold_intervals) get_fold_names() (in module alphagenome.data.fold_intervals) get_gene_interval() (in module alphagenome.data.gene_annotation) get_gene_intervals() (in module alphagenome.data.gene_annotation) get_genes_as_intervals() (alphagenome.data.gene_expression_data.GeneExpressionData method) get_junctions_to_plot() (in module alphagenome.data.junction_data) get_length_for_sequence_name() (alphagenome.io.fasta.FastaExtractor method) get_recommended_scorers() (in module alphagenome.models.v1.variant_scorers) (in module alphagenome.models.v2.variant_scorers) gradients (alphagenome.models.v2.dna_output.InputGradientsOutput attribute) groupby() (alphagenome.data.track_data.TrackData method) H HOMO_SAPIENS (alphagenome.models.v1.dna_client.Organism attribute) (alphagenome.models.v2.dna_client.Organism attribute) I id (alphagenome.data.ontology.OntologyTerm attribute) IG_C_GENE (alphagenome.data.gene_annotation.TranscriptType attribute) IG_C_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) IG_D_GENE (alphagenome.data.gene_annotation.TranscriptType attribute) IG_J_GENE (alphagenome.data.gene_annotation.TranscriptType attribute) IG_J_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) IG_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) IG_V_GENE (alphagenome.data.gene_annotation.TranscriptType attribute) IG_V_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) info (alphagenome.data.genome.Interval attribute) (alphagenome.data.genome.Junction attribute) (alphagenome.data.genome.Variant attribute) (alphagenome.data.transcript.Transcript attribute) InputGradientsOutput (class in alphagenome.models.v2.dna_output) interleave() (in module alphagenome.data.track_data) intersect() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) intersect_intervals() (in module alphagenome.data.genome) intersect_with_interval() (alphagenome.data.junction_data.JunctionData method) interval (alphagenome.data.gene_expression_data.GeneExpressionData attribute) (alphagenome.data.junction_data.JunctionData attribute) (alphagenome.data.track_data.TrackData attribute) (alphagenome.models.v2.dna_output.InputGradientsOutput attribute) (alphagenome.models.v2.dna_output.TargetGeneMetadata attribute) Interval (class in alphagenome.data.genome) IntervalAggregationType (class in alphagenome.models.v1.interval_scorers) (class in alphagenome.models.v2.interval_scorers) IntervalAnnotation (class in alphagenome.visualization.plot_components) is_coding (alphagenome.data.transcript.Transcript attribute) is_deletion (alphagenome.data.genome.Variant attribute) is_frameshift (alphagenome.data.genome.Variant attribute) is_indel (alphagenome.data.genome.Variant attribute) is_insertion (alphagenome.data.genome.Variant attribute) is_mitochondrial (alphagenome.data.transcript.Transcript attribute) is_negative_strand (alphagenome.data.transcript.Transcript attribute) is_positive_strand (alphagenome.data.transcript.Transcript attribute) is_signed (alphagenome.atlas.atlas.ScorerMetadata attribute) (alphagenome.models.v1.variant_scorers.CenterMaskScorer attribute) (alphagenome.models.v1.variant_scorers.ContactMapScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskActiveScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskLFCScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskSplicingScorer attribute) (alphagenome.models.v1.variant_scorers.PolyadenylationScorer attribute) (alphagenome.models.v1.variant_scorers.SpliceJunctionScorer attribute) (alphagenome.models.v2.variant_scorers.CenterMaskScorer attribute) (alphagenome.models.v2.variant_scorers.ContactMapScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskActiveScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskLFCScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskSplicingScorer attribute) (alphagenome.models.v2.variant_scorers.MethylationScorer attribute) (alphagenome.models.v2.variant_scorers.PolyadenylationScorer attribute) (alphagenome.models.v2.variant_scorers.SpliceJunctionScorer attribute) is_snv (alphagenome.data.genome.Variant attribute) is_structural (alphagenome.data.genome.Variant attribute) ism_matrix() (in module alphagenome.interpretation.ism) ism_variants() (in module alphagenome.interpretation.ism) J Junction (class in alphagenome.data.genome) JunctionData (class in alphagenome.data.junction_data) junctions (alphagenome.data.junction_data.JunctionData attribute) K k (alphagenome.data.genome.Junction attribute) L L2_DIFF (alphagenome.models.v1.variant_scorers.AggregationType attribute) (alphagenome.models.v2.variant_scorers.AggregationType attribute) L2_DIFF_LOG1P (alphagenome.models.v1.variant_scorers.AggregationType attribute) (alphagenome.models.v2.variant_scorers.AggregationType attribute) label_color (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute) labels (alphagenome.visualization.plot_components.AbstractAnnotation attribute) LNCRNA (alphagenome.data.gene_annotation.TranscriptType attribute) M map_over_outputs() (alphagenome.models.v2.dna_output.Output method) map_track_data() (alphagenome.models.v1.dna_output.Output method) MAX (alphagenome.data.track_data.AggregationType attribute) MAX_CONDITIONING_CELLS (in module alphagenome.models.v2.dna_client) MEAN (alphagenome.models.v1.interval_scorers.IntervalAggregationType attribute) (alphagenome.models.v2.interval_scorers.IntervalAggregationType attribute) merge_overlapping_intervals() (in module alphagenome.data.genome) metadata (alphagenome.data.junction_data.JunctionData attribute) (alphagenome.data.track_data.TrackData attribute) (alphagenome.models.v1.dna_client.DnaClient attribute) (alphagenome.models.v2.dna_client.DnaClient attribute) methylation (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) METHYLATION (alphagenome.models.v2.dna_output.OutputType attribute) (alphagenome.models.v2.variant_scorers.BaseVariantScorer attribute) MethylationScorer (class in alphagenome.models.v2.variant_scorers) MINIMAL (alphagenome.visualization.plot_transcripts.TranscriptStylePreset attribute) MIRNA (alphagenome.data.gene_annotation.TranscriptType attribute) MISC_RNA (alphagenome.data.gene_annotation.TranscriptType attribute) model_version (alphagenome.models.v1.dna_client.DnaClient attribute) (alphagenome.models.v2.dna_client.DnaClient attribute) ModelCondition (class in alphagenome.models.v2.model_condition) ModelVersion (class in alphagenome.models.v1.dna_client) (class in alphagenome.models.v2.dna_client) module alphagenome.atlas alphagenome.interpretation MT_RRNA (alphagenome.data.gene_annotation.TranscriptType attribute) MT_TRNA (alphagenome.data.gene_annotation.TranscriptType attribute) MUS_MUSCULUS (alphagenome.models.v1.dna_client.Organism attribute) (alphagenome.models.v2.dna_client.Organism attribute) N name (alphagenome.atlas.atlas.ScorerMetadata attribute) (alphagenome.data.genome.Interval attribute) (alphagenome.data.genome.Junction attribute) (alphagenome.data.genome.Variant attribute) (alphagenome.models.v1.interval_scorers.GeneMaskScorer attribute) (alphagenome.models.v1.variant_scorers.CenterMaskScorer attribute) (alphagenome.models.v1.variant_scorers.ContactMapScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskActiveScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskLFCScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskSplicingScorer attribute) (alphagenome.models.v1.variant_scorers.PolyadenylationScorer attribute) (alphagenome.models.v1.variant_scorers.SpliceJunctionScorer attribute) (alphagenome.models.v2.interval_scorers.GeneMaskScorer attribute) (alphagenome.models.v2.variant_scorers.CenterMaskScorer attribute) (alphagenome.models.v2.variant_scorers.ContactMapScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskActiveScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskLFCScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskSplicingScorer attribute) (alphagenome.models.v2.variant_scorers.MethylationScorer attribute) (alphagenome.models.v2.variant_scorers.PolyadenylationScorer attribute) (alphagenome.models.v2.variant_scorers.SpliceJunctionScorer attribute) names (alphagenome.data.gene_expression_data.GeneExpressionData attribute) (alphagenome.data.track_data.TrackData attribute) negative_strand (alphagenome.data.genome.Interval attribute) (alphagenome.data.genome.Junction attribute) NON_STOP_DECAY (alphagenome.data.gene_annotation.TranscriptType attribute) NONSENSE_MEDIATED_DECAY (alphagenome.data.gene_annotation.TranscriptType attribute) normalize_values() (alphagenome.data.junction_data.JunctionData method) normalize_variant() (in module alphagenome.data.genome) ntr (alphagenome.models.v2.model_condition.ModelCondition attribute) num_tracks (alphagenome.data.gene_expression_data.GeneExpressionData attribute) (alphagenome.data.track_data.TrackData attribute) O observed_metadata() (alphagenome.models.v2.dna_client.DnaClient method) offset_in_cds() (alphagenome.data.transcript.Transcript method) ontology_curie (alphagenome.data.ontology.OntologyTerm attribute) ontology_curies (alphagenome.models.v2.model_condition.ModelCondition attribute) ontology_terms (alphagenome.data.track_data.TrackData attribute) (alphagenome.models.v2.model_condition.ModelCondition attribute) OntologyTerm (class in alphagenome.data.ontology) OntologyType (class in alphagenome.data.ontology) Organism (class in alphagenome.models.v1.dna_client) (class in alphagenome.models.v2.dna_client) Output (class in alphagenome.models.v1.dna_output) (class in alphagenome.models.v2.dna_output) output_metadata() (alphagenome.models.v1.dna_client.DnaClient method) output_type (alphagenome.models.v2.dna_output.InputGradientsOutput attribute) OutputMetadata (class in alphagenome.models.v1.dna_output) (class in alphagenome.models.v2.dna_output) OutputType (class in alphagenome.models.v1.dna_output) (class in alphagenome.models.v2.dna_output) OverlaidGeneExpression (class in alphagenome.visualization.plot_components) OverlaidTracks (class in alphagenome.visualization.plot_components) overlap_ranges() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) overlaps() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) P PA_QTL (alphagenome.models.v1.variant_scorers.BaseVariantScorer attribute) (alphagenome.models.v2.variant_scorers.BaseVariantScorer attribute) pad() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) (alphagenome.data.track_data.TrackData method) pad_track() (in module alphagenome.visualization.plot) plot() (in module alphagenome.visualization.plot_components) plot_ax() (alphagenome.visualization.plot_components.AbstractAnnotation method) (alphagenome.visualization.plot_components.AbstractComponent method) (alphagenome.visualization.plot_components.ContactMaps method) (alphagenome.visualization.plot_components.ContactMapsDiff method) (alphagenome.visualization.plot_components.EmptyComponent method) (alphagenome.visualization.plot_components.EnhancerArcs method) (alphagenome.visualization.plot_components.FeatureContribution method) (alphagenome.visualization.plot_components.GeneExpression method) (alphagenome.visualization.plot_components.IntervalAnnotation method) (alphagenome.visualization.plot_components.OverlaidGeneExpression method) (alphagenome.visualization.plot_components.OverlaidTracks method) (alphagenome.visualization.plot_components.Sashimi method) (alphagenome.visualization.plot_components.ScoreBar method) (alphagenome.visualization.plot_components.SeqLogo method) (alphagenome.visualization.plot_components.Tracks method) (alphagenome.visualization.plot_components.TranscriptAnnotation method) (alphagenome.visualization.plot_components.VariantAnnotation method) plot_contact_map() (in module alphagenome.visualization.plot) plot_labels() (alphagenome.visualization.plot_components.AbstractAnnotation method) (alphagenome.visualization.plot_components.IntervalAnnotation method) (alphagenome.visualization.plot_components.VariantAnnotation method) plot_track() (in module alphagenome.visualization.plot) plot_tracks() (in module alphagenome.visualization.plot) plot_transcripts() (in module alphagenome.visualization.plot_transcripts) PolyadenylationScorer (class in alphagenome.models.v1.variant_scorers) (class in alphagenome.models.v2.variant_scorers) position (alphagenome.data.genome.Variant attribute) positional_axes (alphagenome.data.track_data.TrackData attribute) predict_interval() (alphagenome.models.v1.dna_client.DnaClient method) (alphagenome.models.v2.dna_client.DnaClient method) predict_interval_gradients() (alphagenome.models.v2.dna_client.DnaClient method) predict_interval_gradients_batch() (alphagenome.models.v2.dna_client.DnaClient method) predict_intervals() (alphagenome.models.v1.dna_client.DnaClient method) (alphagenome.models.v2.dna_client.DnaClient method) predict_sequence() (alphagenome.models.v1.dna_client.DnaClient method) (alphagenome.models.v2.dna_client.DnaClient method) predict_sequences() (alphagenome.models.v1.dna_client.DnaClient method) (alphagenome.models.v2.dna_client.DnaClient method) predict_variant() (alphagenome.models.v1.dna_client.DnaClient method) (alphagenome.models.v2.dna_client.DnaClient method) predict_variants() (alphagenome.models.v1.dna_client.DnaClient method) (alphagenome.models.v2.dna_client.DnaClient method) procap (alphagenome.models.v1.dna_output.Output attribute) (alphagenome.models.v1.dna_output.OutputMetadata attribute) PROCAP (alphagenome.models.v1.dna_output.OutputType attribute) PROCESSED_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) PROCESSED_TRANSCRIPT (alphagenome.data.gene_annotation.TranscriptType attribute) PROTEIN_CODING (alphagenome.data.gene_annotation.TranscriptType attribute) PROTEIN_CODING_CDS_NOT_DEFINED (alphagenome.data.gene_annotation.TranscriptType attribute) PROTEIN_CODING_LOF (alphagenome.data.gene_annotation.TranscriptType attribute) protein_id (alphagenome.data.transcript.Transcript attribute) Q query_interval() (alphagenome.atlas.atlas.AtlasClient method) query_variant() (alphagenome.atlas.atlas.AtlasClient method) query_variants() (alphagenome.atlas.atlas.AtlasClient method) R RECOMMENDED_VARIANT_SCORERS (in module alphagenome.models.v1.variant_scorers) (in module alphagenome.models.v2.variant_scorers) reference (alphagenome.models.v1.dna_output.VariantOutput attribute) (alphagenome.models.v2.dna_output.VariantOutput attribute) reference_bases (alphagenome.data.genome.Variant attribute) reference_interval (alphagenome.data.genome.Variant attribute) reference_overlaps() (alphagenome.data.genome.Variant method) requested_output (alphagenome.models.v1.interval_scorers.GeneMaskScorer attribute) (alphagenome.models.v1.variant_scorers.CenterMaskScorer attribute) (alphagenome.models.v1.variant_scorers.ContactMapScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskActiveScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskLFCScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskSplicingScorer attribute) (alphagenome.models.v2.interval_scorers.GeneMaskScorer attribute) (alphagenome.models.v2.variant_scorers.CenterMaskScorer attribute) (alphagenome.models.v2.variant_scorers.ContactMapScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskActiveScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskLFCScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskSplicingScorer attribute) (alphagenome.models.v2.variant_scorers.MethylationScorer attribute) resize() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) (alphagenome.data.track_data.TrackData method) (alphagenome.models.v1.dna_output.Output method) (alphagenome.models.v2.dna_output.Output method) resolution (alphagenome.data.track_data.TrackData attribute) RETAINED_INTRON (alphagenome.data.gene_annotation.TranscriptType attribute) reverse_complement() (alphagenome.data.track_data.TrackData method) (in module alphagenome.io.fasta) RIBOZYME (alphagenome.data.gene_annotation.TranscriptType attribute) rna_seq (alphagenome.models.v1.dna_output.Output attribute) (alphagenome.models.v1.dna_output.OutputMetadata attribute) RNA_SEQ (alphagenome.models.v1.dna_output.OutputType attribute) rna_seq (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) RNA_SEQ (alphagenome.models.v2.dna_output.OutputType attribute) RRNA (alphagenome.data.gene_annotation.TranscriptType attribute) RRNA_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) S Sashimi (class in alphagenome.visualization.plot_components) sashimi_plot() (in module alphagenome.visualization.plot) sc_atac (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) SC_ATAC (alphagenome.models.v2.dna_output.OutputType attribute) sc_gene_expression (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) SC_GENE_EXPRESSION (alphagenome.models.v2.dna_output.OutputType attribute) sc_gene_expression_denoised (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) SC_GENE_EXPRESSION_DENOISED (alphagenome.models.v2.dna_output.OutputType attribute) scalar_score (alphagenome.models.v2.dna_output.InputGradientsOutput attribute) SCARNA (alphagenome.data.gene_annotation.TranscriptType attribute) score_enhancers() (in module alphagenome.interpretation.enhancer_scoring) score_interval() (alphagenome.models.v1.dna_client.DnaClient method) (alphagenome.models.v2.dna_client.DnaClient method) score_intervals() (alphagenome.models.v1.dna_client.DnaClient method) (alphagenome.models.v2.dna_client.DnaClient method) score_ism_variants() (alphagenome.models.v1.dna_client.DnaClient method) (alphagenome.models.v2.dna_client.DnaClient method) score_variant() (alphagenome.models.v1.dna_client.DnaClient method) (alphagenome.models.v2.dna_client.DnaClient method) score_variants() (alphagenome.models.v1.dna_client.DnaClient method) (alphagenome.models.v2.dna_client.DnaClient method) ScoreBar (class in alphagenome.visualization.plot_components) scorer_metadata() (alphagenome.atlas.atlas.AtlasClient method) ScorerMetadata (class in alphagenome.atlas.atlas) SCRNA (alphagenome.data.gene_annotation.TranscriptType attribute) select_tracks_by_index() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.track_data.TrackData method) select_tracks_by_name() (alphagenome.data.track_data.TrackData method) selenocysteine_pos_in_protein (alphagenome.data.transcript.Transcript attribute) selenocysteines (alphagenome.data.transcript.Transcript attribute) SeqLogo (class in alphagenome.visualization.plot_components) seqlogo() (in module alphagenome.visualization.plot) SEQUENCE_LENGTH_100KB (in module alphagenome.models.v1.dna_client) (in module alphagenome.models.v2.dna_client) SEQUENCE_LENGTH_16KB (in module alphagenome.models.v1.dna_client) (in module alphagenome.models.v2.dna_client) SEQUENCE_LENGTH_1MB (in module alphagenome.models.v1.dna_client) (in module alphagenome.models.v2.dna_client) SEQUENCE_LENGTH_500KB (in module alphagenome.models.v1.dna_client) (in module alphagenome.models.v2.dna_client) sequence_names (alphagenome.io.fasta.FastaExtractor attribute) shift() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) slice_by_interval() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.track_data.TrackData method) slice_by_positions() (alphagenome.data.track_data.TrackData method) SNORNA (alphagenome.data.gene_annotation.TranscriptType attribute) SNRNA (alphagenome.data.gene_annotation.TranscriptType attribute) splice_acceptor_sites (alphagenome.data.transcript.Transcript attribute) splice_acceptors (alphagenome.data.transcript.Transcript attribute) splice_donor_sites (alphagenome.data.transcript.Transcript attribute) splice_donors (alphagenome.data.transcript.Transcript attribute) SPLICE_JUNCTION (alphagenome.models.v1.variant_scorers.BaseVariantScorer attribute) (alphagenome.models.v2.variant_scorers.BaseVariantScorer attribute) splice_junctions (alphagenome.models.v1.dna_output.Output attribute) (alphagenome.models.v1.dna_output.OutputMetadata attribute) SPLICE_JUNCTIONS (alphagenome.models.v1.dna_output.OutputType attribute) splice_junctions (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) SPLICE_JUNCTIONS (alphagenome.models.v2.dna_output.OutputType attribute) splice_regions (alphagenome.data.transcript.Transcript attribute) splice_site_usage (alphagenome.models.v1.dna_output.Output attribute) (alphagenome.models.v1.dna_output.OutputMetadata attribute) SPLICE_SITE_USAGE (alphagenome.models.v1.dna_output.OutputType attribute) splice_site_usage (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) SPLICE_SITE_USAGE (alphagenome.models.v2.dna_output.OutputType attribute) splice_sites (alphagenome.models.v1.dna_output.Output attribute) (alphagenome.models.v1.dna_output.OutputMetadata attribute) SPLICE_SITES (alphagenome.models.v1.dna_output.OutputType attribute) splice_sites (alphagenome.models.v2.dna_output.Output attribute) (alphagenome.models.v2.dna_output.OutputMetadata attribute) SPLICE_SITES (alphagenome.models.v2.dna_output.OutputType attribute) SpliceJunctionScorer (class in alphagenome.models.v1.variant_scorers) (class in alphagenome.models.v2.variant_scorers) split() (alphagenome.data.genome.Variant method) SRNA (alphagenome.data.gene_annotation.TranscriptType attribute) STANDARD (alphagenome.visualization.plot_transcripts.TranscriptStylePreset attribute) start (alphagenome.data.genome.Interval attribute) (alphagenome.data.genome.Junction attribute) (alphagenome.data.genome.Variant attribute) start_codon (alphagenome.data.transcript.Transcript attribute) stop_codon (alphagenome.data.transcript.Transcript attribute) strand (alphagenome.data.genome.Interval attribute) (alphagenome.data.genome.Junction attribute) (alphagenome.data.transcript.Transcript attribute) Strand (class in alphagenome.data.genome) strand_int (alphagenome.data.transcript.Transcript attribute) strands (alphagenome.data.gene_expression_data.GeneExpressionData attribute) (alphagenome.data.track_data.TrackData attribute) subsample() (in module alphagenome.models.v2.gene_counts_condition) Subset (class in alphagenome.data.fold_intervals) SUM (alphagenome.data.track_data.AggregationType attribute) (alphagenome.models.v1.interval_scorers.IntervalAggregationType attribute) (alphagenome.models.v2.interval_scorers.IntervalAggregationType attribute) supported_conditions() (alphagenome.models.v2.dna_client.DnaClient method) swap_strand() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) T target_gene (alphagenome.models.v2.dna_output.InputGradientsOutput attribute) TargetGeneMetadata (class in alphagenome.models.v2.dna_output) TEC (alphagenome.data.gene_annotation.TranscriptType attribute) TEST (alphagenome.data.fold_intervals.Subset attribute) tidy_anndata() (in module alphagenome.models.v1.variant_scorers) (in module alphagenome.models.v2.variant_scorers) tidy_scores() (in module alphagenome.models.v1.variant_scorers) (in module alphagenome.models.v2.variant_scorers) tile_interval() (in module alphagenome.interpretation.enhancer_scoring) to_anndata() (alphagenome.data.gene_expression_data.GeneExpressionData method) to_dict() (alphagenome.data.genome.Variant method) to_interval_dict() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) to_proto() (alphagenome.models.v1.interval_scorers.GeneMaskScorer method) (alphagenome.models.v1.interval_scorers.IntervalAggregationType method) (alphagenome.models.v1.variant_scorers.AggregationType method) (alphagenome.models.v1.variant_scorers.CenterMaskScorer method) (alphagenome.models.v1.variant_scorers.ContactMapScorer method) (alphagenome.models.v1.variant_scorers.GeneMaskActiveScorer method) (alphagenome.models.v1.variant_scorers.GeneMaskLFCScorer method) (alphagenome.models.v1.variant_scorers.GeneMaskSplicingScorer method) (alphagenome.models.v1.variant_scorers.PolyadenylationScorer method) (alphagenome.models.v1.variant_scorers.SpliceJunctionScorer method) (alphagenome.models.v2.interval_scorers.GeneMaskScorer method) (alphagenome.models.v2.interval_scorers.IntervalAggregationType method) (alphagenome.models.v2.variant_scorers.AggregationType method) (alphagenome.models.v2.variant_scorers.CenterMaskScorer method) (alphagenome.models.v2.variant_scorers.ContactMapScorer method) (alphagenome.models.v2.variant_scorers.GeneMaskActiveScorer method) (alphagenome.models.v2.variant_scorers.GeneMaskLFCScorer method) (alphagenome.models.v2.variant_scorers.GeneMaskSplicingScorer method) (alphagenome.models.v2.variant_scorers.MethylationScorer method) (alphagenome.models.v2.variant_scorers.PolyadenylationScorer method) (alphagenome.models.v2.variant_scorers.SpliceJunctionScorer method) to_regex() (alphagenome.data.genome.VariantFormat method) to_track_data() (alphagenome.models.v2.dna_output.InputGradientsOutput method) TR_C_GENE (alphagenome.data.gene_annotation.TranscriptType attribute) TR_D_GENE (alphagenome.data.gene_annotation.TranscriptType attribute) TR_J_GENE (alphagenome.data.gene_annotation.TranscriptType attribute) TR_J_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) TR_V_GENE (alphagenome.data.gene_annotation.TranscriptType attribute) TR_V_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) track_metadata (alphagenome.atlas.atlas.ScorerMetadata attribute) (alphagenome.data.gene_expression_data.GeneExpressionData attribute) (alphagenome.models.v2.dna_output.InputGradientsOutput attribute) TrackData (class in alphagenome.data.track_data) Tracks (class in alphagenome.visualization.plot_components) TRAIN (alphagenome.data.fold_intervals.Subset attribute) TRANSCRIBED_PROCESSED_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) TRANSCRIBED_UNITARY_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) TRANSCRIBED_UNPROCESSED_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) Transcript (class in alphagenome.data.transcript) transcript_id (alphagenome.data.transcript.Transcript attribute) transcript_interval (alphagenome.data.transcript.Transcript attribute) TranscriptAnnotation (class in alphagenome.visualization.plot_components) TranscriptExtractor (class in alphagenome.data.transcript) TranscriptStyle (class in alphagenome.visualization.plot_transcripts) TranscriptStylePreset (class in alphagenome.visualization.plot_transcripts) TranscriptType (class in alphagenome.data.gene_annotation) TRANSLATED_PROCESSED_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) truncate() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) type (alphagenome.data.ontology.OntologyTerm attribute) U uberon (alphagenome.models.v2.model_condition.ModelCondition attribute) union_intervals() (in module alphagenome.data.genome) uniprot_id (alphagenome.data.transcript.Transcript attribute) UNITARY_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) UNPROCESSED_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) uns (alphagenome.data.junction_data.JunctionData attribute) (alphagenome.data.track_data.TrackData attribute) upsample() (alphagenome.data.track_data.TrackData method) use_default_labels (alphagenome.visualization.plot_components.AbstractAnnotation attribute) utr3 (alphagenome.data.transcript.Transcript attribute) utr3_color (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute) utr5 (alphagenome.data.transcript.Transcript attribute) utr5_color (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute) utr_height (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute) V VALID (alphagenome.data.fold_intervals.Subset attribute) validate_sequence_length() (in module alphagenome.models.v1.dna_client) (in module alphagenome.models.v2.dna_client) values (alphagenome.data.gene_expression_data.GeneExpressionData attribute) (alphagenome.data.junction_data.JunctionData attribute) (alphagenome.data.track_data.TrackData attribute) Variant (class in alphagenome.data.genome) VariantAnnotation (class in alphagenome.visualization.plot_components) VariantFormat (class in alphagenome.data.genome) VariantOutput (class in alphagenome.models.v1.dna_output) (class in alphagenome.models.v2.dna_output) VariantScorerTypes (in module alphagenome.models.v1.variant_scorers) (in module alphagenome.models.v2.variant_scorers) VAULT_RNA (alphagenome.data.gene_annotation.TranscriptType attribute) W width (alphagenome.data.genome.Interval attribute) (alphagenome.data.track_data.TrackData attribute) (alphagenome.models.v1.interval_scorers.GeneMaskScorer attribute) (alphagenome.models.v1.variant_scorers.CenterMaskScorer attribute) (alphagenome.models.v1.variant_scorers.GeneMaskSplicingScorer attribute) (alphagenome.models.v2.interval_scorers.GeneMaskScorer attribute) (alphagenome.models.v2.variant_scorers.CenterMaskScorer attribute) (alphagenome.models.v2.variant_scorers.GeneMaskSplicingScorer attribute) (alphagenome.models.v2.variant_scorers.MethylationScorer attribute) with_metadata_column() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.junction_data.JunctionData method) (alphagenome.data.track_data.TrackData method) (alphagenome.models.v2.dna_output.Output method) with_name_suffix() (alphagenome.data.gene_expression_data.GeneExpressionData method) (alphagenome.data.junction_data.JunctionData method) (alphagenome.data.track_data.TrackData method) (alphagenome.models.v2.dna_output.Output method) within_reference() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Junction method) X xlim_pad (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute)