Index

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.variant_scorers.AggregationType attribute), [1] ACTIVE_SUM (alphagenome.models.variant_scorers.AggregationType attribute), [1] add_label() (alphagenome.visualization.plot_components.AbstractAnnotation method) aggregation_type (alphagenome.models.variant_scorers.CenterMaskScorer attribute), [1] AggregationType (class in alphagenome.models.variant_scorers) ALL_FOLDS (alphagenome.models.dna_client.ModelVersion attribute) alphagenome.interpretation module

alternate (alphagenome.models.dna_output.VariantOutput attribute), [1] alternate_bases (alphagenome.data.genome.Variant attribute), [1] alternate_overlaps() (alphagenome.data.genome.Variant method) annotations (alphagenome.visualization.plot_components.AbstractAnnotation attribute) ARTIFACT (alphagenome.data.gene_annotation.TranscriptType attribute) as_integer_ratio() (alphagenome.data.genome.Strand method) (alphagenome.data.ontology.OntologyType method) as_truncated_str() (alphagenome.data.genome.Variant method) as_unstranded() (alphagenome.data.genome.Interval method) atac (alphagenome.models.dna_output.Output attribute), [1] (alphagenome.models.dna_output.OutputMetadata attribute), [1] ATAC (alphagenome.models.dna_output.OutputType attribute), [1]

B

base_variant_scorer (alphagenome.models.variant_scorers.CenterMaskScorer attribute), [1] (alphagenome.models.variant_scorers.ContactMapScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskActiveScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskLFCScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskSplicingScorer attribute), [1] (alphagenome.models.variant_scorers.PolyadenylationScorer attribute), [1] (alphagenome.models.variant_scorers.SpliceJunctionScorer attribute), [1] BaseVariantScorer (class in alphagenome.models.variant_scorers)

bin_index() (alphagenome.data.track_data.TrackData method) binary_mask() (alphagenome.data.genome.Interval method) binary_mask_stranded() (alphagenome.data.genome.Interval method) bit_count() (alphagenome.data.genome.Strand method) (alphagenome.data.ontology.OntologyType method) bit_length() (alphagenome.data.genome.Strand method) (alphagenome.data.ontology.OntologyType method) boundary_shift() (alphagenome.data.genome.Interval method)

C

cache_transcripts() (alphagenome.data.transcript.TranscriptExtractor method) cage (alphagenome.models.dna_output.Output attribute), [1] (alphagenome.models.dna_output.OutputMetadata attribute), [1] CAGE (alphagenome.models.dna_output.OutputType attribute), [1] cds (alphagenome.data.transcript.Transcript attribute), [1] cds_color (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute), [1] cds_height (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute), [1] cds_including_stop_codon (alphagenome.data.transcript.Transcript attribute), [1] center() (alphagenome.data.genome.Interval method) CENTER_MASK (alphagenome.models.variant_scorers.BaseVariantScorer attribute), [1] CenterMaskScorer (class in alphagenome.models.variant_scorers) change_resolution() (alphagenome.data.track_data.TrackData method) channel (alphagenome.models.dna_client.DnaClient attribute) chip_histone (alphagenome.models.dna_output.Output attribute), [1] (alphagenome.models.dna_output.OutputMetadata attribute), [1] CHIP_HISTONE (alphagenome.models.dna_output.OutputType attribute), [1] chip_tf (alphagenome.models.dna_output.Output attribute), [1] (alphagenome.models.dna_output.OutputMetadata attribute), [1] CHIP_TF (alphagenome.models.dna_output.OutputType attribute), [1] chromosome (alphagenome.data.genome.Interval attribute), [1] (alphagenome.data.genome.Junction attribute), [1] (alphagenome.data.genome.Variant attribute), [1] (alphagenome.data.transcript.Transcript attribute), [1]

CL (alphagenome.data.ontology.OntologyType attribute) CLO (alphagenome.data.ontology.OntologyType attribute) colors (alphagenome.visualization.plot_components.AbstractAnnotation attribute) concat() (in module alphagenome.data.track_data) concatenate() (alphagenome.models.dna_output.OutputMetadata method) conjugate() (alphagenome.data.genome.Strand method) (alphagenome.data.ontology.OntologyType method) CONTACT_MAP (alphagenome.models.variant_scorers.BaseVariantScorer attribute), [1] contact_maps (alphagenome.models.dna_output.Output attribute), [1] (alphagenome.models.dna_output.OutputMetadata attribute), [1] CONTACT_MAPS (alphagenome.models.dna_output.OutputType attribute), [1] ContactMaps (class in alphagenome.visualization.plot_components) ContactMapScorer (class in alphagenome.models.variant_scorers) ContactMapsDiff (class in alphagenome.visualization.plot_components) contains() (alphagenome.data.genome.Interval method) copy() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Variant method) (alphagenome.data.track_data.TrackData method) coverage() (alphagenome.data.genome.Interval method) coverage_stranded() (alphagenome.data.genome.Interval method)

D

denominator (alphagenome.data.genome.Strand attribute) (alphagenome.data.ontology.OntologyType attribute) DIFF_LOG2_SUM (alphagenome.models.variant_scorers.AggregationType attribute), [1] DIFF_MEAN (alphagenome.models.variant_scorers.AggregationType attribute), [1] DIFF_SUM (alphagenome.models.variant_scorers.AggregationType attribute), [1] DIFF_SUM_LOG2 (alphagenome.models.variant_scorers.AggregationType attribute), [1] dinucleotide_region() (alphagenome.data.genome.Junction method) DnaClient (class in alphagenome.models.dna_client)

dnase (alphagenome.models.dna_output.Output attribute), [1] (alphagenome.models.dna_output.OutputMetadata attribute), [1] DNASE (alphagenome.models.dna_output.OutputType attribute), [1] 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.data.ontology.OntologyType attribute) EmptyComponent (class in alphagenome.visualization.plot_components) end (alphagenome.data.genome.Interval attribute), [1] (alphagenome.data.genome.Junction attribute), [1] (alphagenome.data.genome.Variant attribute)

exons (alphagenome.data.transcript.Transcript attribute), [1] extract() (alphagenome.data.transcript.TranscriptExtractor method) extract_tss() (in module alphagenome.data.gene_annotation)

F

filter_ontology_terms() (alphagenome.models.dna_output.Output method) filter_output_type() (alphagenome.models.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_negative_strand() (alphagenome.data.track_data.TrackData method) filter_to_nonnegative_strand() (alphagenome.data.track_data.TrackData method) filter_to_nonpositive_strand() (alphagenome.data.track_data.TrackData method) filter_to_positive_strand() (alphagenome.data.track_data.TrackData method) filter_to_strand() (alphagenome.models.dna_output.Output method) filter_to_stranded() (alphagenome.data.track_data.TrackData method) filter_to_unstranded() (alphagenome.data.track_data.TrackData method) filter_tracks() (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), [1] fix_truncation() (alphagenome.data.transcript.Transcript class method)

FOLD_0 (alphagenome.models.dna_client.ModelVersion attribute) FOLD_1 (alphagenome.models.dna_client.ModelVersion attribute) FOLD_2 (alphagenome.models.dna_client.ModelVersion attribute) FOLD_3 (alphagenome.models.dna_client.ModelVersion attribute) from_bytes() (alphagenome.data.genome.Strand method) (alphagenome.data.ontology.OntologyType method) 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) from_proto() (alphagenome.data.genome.Interval class method) (alphagenome.data.genome.Strand class method) (alphagenome.data.genome.Variant class method) from_protos() (in module alphagenome.data.track_data) from_pyranges_dict() (alphagenome.data.genome.Interval class method) from_str() (alphagenome.data.genome.Interval class method) (alphagenome.data.genome.Strand class method) (alphagenome.data.genome.Variant class method)

G

gene_id (alphagenome.data.transcript.Transcript attribute), [1] GENE_MASK_ACTIVE (alphagenome.models.variant_scorers.BaseVariantScorer attribute), [1] GENE_MASK_LFC (alphagenome.models.variant_scorers.BaseVariantScorer attribute), [1] GENE_MASK_SPLICING (alphagenome.models.variant_scorers.BaseVariantScorer attribute), [1] GeneMaskActiveScorer (class in alphagenome.models.variant_scorers) GeneMaskLFCScorer (class in alphagenome.models.variant_scorers) GeneMaskSplicingScorer (class in alphagenome.models.variant_scorers) get() (alphagenome.models.dna_output.Output method) (alphagenome.models.dna_output.OutputMetadata method) get_all_folds() (in module alphagenome.data.fold_intervals) get_ax_height() (alphagenome.visualization.plot_components.AbstractComponent method) (alphagenome.visualization.plot_components.ContactMaps method) (alphagenome.visualization.plot_components.EmptyComponent method) (alphagenome.visualization.plot_components.OverlaidTracks method) (alphagenome.visualization.plot_components.Sashimi 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_recommended_scorers() (in module alphagenome.models.variant_scorers) groupby() (alphagenome.data.track_data.TrackData method)

H

has_labels (alphagenome.visualization.plot_components.AbstractAnnotation attribute) (alphagenome.visualization.plot_components.IntervalAnnotation attribute) (alphagenome.visualization.plot_components.VariantAnnotation attribute)

HOMO_SAPIENS (alphagenome.models.dna_client.Organism attribute)

I

id (alphagenome.data.ontology.OntologyTerm attribute), [1] 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) imag (alphagenome.data.genome.Strand attribute) (alphagenome.data.ontology.OntologyType attribute) info (alphagenome.data.genome.Interval attribute), [1] (alphagenome.data.genome.Junction attribute), [1] (alphagenome.data.genome.Variant attribute), [1] (alphagenome.data.transcript.Transcript attribute), [1] interleave() (in module alphagenome.data.track_data) intersect() (alphagenome.data.genome.Interval method) interval (alphagenome.data.track_data.TrackData attribute), [1]

Interval (class in alphagenome.data.genome) IntervalAnnotation (class in alphagenome.visualization.plot_components) introns (alphagenome.data.transcript.Transcript attribute) is_coding (alphagenome.data.transcript.Transcript attribute), [1] is_mitochondrial (alphagenome.data.transcript.Transcript attribute), [1] is_negative_strand (alphagenome.data.transcript.Transcript attribute), [1] is_positive_strand (alphagenome.data.transcript.Transcript attribute), [1] is_signed (alphagenome.models.variant_scorers.CenterMaskScorer attribute), [1] (alphagenome.models.variant_scorers.ContactMapScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskActiveScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskLFCScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskSplicingScorer attribute), [1] (alphagenome.models.variant_scorers.PolyadenylationScorer attribute), [1] (alphagenome.models.variant_scorers.SpliceJunctionScorer attribute), [1] is_variant (alphagenome.visualization.plot_components.AbstractAnnotation attribute) (alphagenome.visualization.plot_components.IntervalAnnotation attribute) (alphagenome.visualization.plot_components.VariantAnnotation attribute) ism_matrix() (in module alphagenome.interpretation.ism) ism_variants() (in module alphagenome.interpretation.ism)

J

Junction (class in alphagenome.data.genome)

K

k (alphagenome.data.genome.Junction attribute), [1]

L

L2_DIFF (alphagenome.models.variant_scorers.AggregationType attribute), [1] label_color (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute), [1]

labels (alphagenome.visualization.plot_components.AbstractAnnotation attribute) LNCRNA (alphagenome.data.gene_annotation.TranscriptType attribute)

M

map_track_data() (alphagenome.models.dna_output.Output method) metadata (alphagenome.data.track_data.TrackData attribute), [1] (alphagenome.models.dna_client.DnaClient attribute) metadata_from_proto() (in module alphagenome.data.track_data) metadata_to_proto() (in module alphagenome.data.track_data) MINIMAL (alphagenome.visualization.plot_transcripts.TranscriptStylePreset attribute), [1] MIRNA (alphagenome.data.gene_annotation.TranscriptType attribute)

MISC_RNA (alphagenome.data.gene_annotation.TranscriptType attribute) model_version (alphagenome.models.dna_client.DnaClient attribute) ModelVersion (class in alphagenome.models.dna_client) module alphagenome.interpretation MT_RRNA (alphagenome.data.gene_annotation.TranscriptType attribute) MT_TRNA (alphagenome.data.gene_annotation.TranscriptType attribute) MUS_MUSCULUS (alphagenome.models.dna_client.Organism attribute)

N

name (alphagenome.data.genome.Interval attribute), [1] (alphagenome.data.genome.Junction attribute), [1] (alphagenome.data.genome.Variant attribute), [1] (alphagenome.models.variant_scorers.CenterMaskScorer attribute), [1] (alphagenome.models.variant_scorers.ContactMapScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskActiveScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskLFCScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskSplicingScorer attribute), [1] (alphagenome.models.variant_scorers.PolyadenylationScorer attribute), [1] (alphagenome.models.variant_scorers.SpliceJunctionScorer attribute), [1] names (alphagenome.data.track_data.TrackData attribute) NEGATIVE (alphagenome.data.genome.Strand attribute) negative_strand (alphagenome.data.genome.Interval attribute), [1] (alphagenome.data.genome.Junction attribute)

NON_STOP_DECAY (alphagenome.data.gene_annotation.TranscriptType attribute) NONSENSE_MEDIATED_DECAY (alphagenome.data.gene_annotation.TranscriptType attribute) NTR (alphagenome.data.ontology.OntologyType attribute) num_axes (alphagenome.visualization.plot_components.AbstractComponent attribute) (alphagenome.visualization.plot_components.ContactMaps attribute) (alphagenome.visualization.plot_components.ContactMapsDiff attribute) (alphagenome.visualization.plot_components.EmptyComponent attribute) (alphagenome.visualization.plot_components.OverlaidTracks attribute) (alphagenome.visualization.plot_components.Sashimi attribute) (alphagenome.visualization.plot_components.SeqLogo attribute) (alphagenome.visualization.plot_components.Tracks attribute) (alphagenome.visualization.plot_components.TranscriptAnnotation attribute) num_tracks (alphagenome.data.track_data.TrackData attribute) numerator (alphagenome.data.genome.Strand attribute) (alphagenome.data.ontology.OntologyType attribute)

O

offset_in_cds() (alphagenome.data.transcript.Transcript method) ontology_curie (alphagenome.data.ontology.OntologyTerm attribute) ontology_terms (alphagenome.data.track_data.TrackData attribute) OntologyTerm (class in alphagenome.data.ontology) OntologyType (class in alphagenome.data.ontology) Organism (class in alphagenome.models.dna_client)

Output (class in alphagenome.models.dna_output) output_metadata() (alphagenome.models.dna_client.DnaClient method) OutputMetadata (class in alphagenome.models.dna_output) OutputType (class in alphagenome.models.dna_output) OverlaidTracks (class in alphagenome.visualization.plot_components) overlap_ranges() (alphagenome.data.genome.Interval method) overlaps() (alphagenome.data.genome.Interval method)

P

PA_QTL (alphagenome.models.variant_scorers.BaseVariantScorer attribute), [1] pad() (alphagenome.data.genome.Interval method) (alphagenome.data.track_data.TrackData method) pad_inplace() (alphagenome.data.genome.Interval 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.EmptyComponent method) (alphagenome.visualization.plot_components.IntervalAnnotation method) (alphagenome.visualization.plot_components.OverlaidTracks method) (alphagenome.visualization.plot_components.Sashimi 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.variant_scorers) position (alphagenome.data.genome.Variant attribute), [1] positional_axes (alphagenome.data.track_data.TrackData attribute) POSITIVE (alphagenome.data.genome.Strand attribute) predict_interval() (alphagenome.models.dna_client.DnaClient method) predict_intervals() (alphagenome.models.dna_client.DnaClient method) predict_sequence() (alphagenome.models.dna_client.DnaClient method) predict_sequences() (alphagenome.models.dna_client.DnaClient method) predict_variant() (alphagenome.models.dna_client.DnaClient method) predict_variants() (alphagenome.models.dna_client.DnaClient method) procap (alphagenome.models.dna_output.Output attribute), [1] (alphagenome.models.dna_output.OutputMetadata attribute), [1] PROCAP (alphagenome.models.dna_output.OutputType attribute), [1] 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), [1]

R

real (alphagenome.data.genome.Strand attribute) (alphagenome.data.ontology.OntologyType attribute) reference (alphagenome.models.dna_output.VariantOutput attribute), [1] reference_bases (alphagenome.data.genome.Variant attribute), [1] reference_interval (alphagenome.data.genome.Variant attribute) reference_overlaps() (alphagenome.data.genome.Variant method) requested_output (alphagenome.models.variant_scorers.CenterMaskScorer attribute), [1] (alphagenome.models.variant_scorers.ContactMapScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskActiveScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskLFCScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskSplicingScorer attribute), [1] (alphagenome.models.variant_scorers.PolyadenylationScorer attribute) (alphagenome.models.variant_scorers.SpliceJunctionScorer attribute)

resize() (alphagenome.data.genome.Interval method) (alphagenome.data.track_data.TrackData method) (alphagenome.models.dna_output.Output method) resize_inplace() (alphagenome.data.genome.Interval method) resolution (alphagenome.data.track_data.TrackData attribute), [1] RETAINED_INTRON (alphagenome.data.gene_annotation.TranscriptType attribute) reverse_complement() (alphagenome.data.track_data.TrackData method) RIBOZYME (alphagenome.data.gene_annotation.TranscriptType attribute) rna_seq (alphagenome.models.dna_output.Output attribute), [1] (alphagenome.models.dna_output.OutputMetadata attribute), [1] RNA_SEQ (alphagenome.models.dna_output.OutputType attribute), [1] 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) SCARNA (alphagenome.data.gene_annotation.TranscriptType attribute) score_interval() (alphagenome.models.dna_client.DnaClient method) score_intervals() (alphagenome.models.dna_client.DnaClient method) score_ism_variants() (alphagenome.models.dna_client.DnaClient method) score_variant() (alphagenome.models.dna_client.DnaClient method) score_variants() (alphagenome.models.dna_client.DnaClient method) SCRNA (alphagenome.data.gene_annotation.TranscriptType attribute) select_tracks_by_index() (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), [1] selenocysteines (alphagenome.data.transcript.Transcript attribute), [1] SeqLogo (class in alphagenome.visualization.plot_components) seqlogo() (in module alphagenome.visualization.plot) shift() (alphagenome.data.genome.Interval method) slice_by_interval() (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), [1] splice_acceptors (alphagenome.data.transcript.Transcript attribute), [1] splice_donor_sites (alphagenome.data.transcript.Transcript attribute), [1] splice_donors (alphagenome.data.transcript.Transcript attribute), [1] SPLICE_JUNCTION (alphagenome.models.variant_scorers.BaseVariantScorer attribute), [1] splice_junctions (alphagenome.models.dna_output.Output attribute), [1] (alphagenome.models.dna_output.OutputMetadata attribute), [1]

SPLICE_JUNCTIONS (alphagenome.models.dna_output.OutputType attribute), [1] splice_regions (alphagenome.data.transcript.Transcript attribute), [1] splice_site_usage (alphagenome.models.dna_output.Output attribute), [1] (alphagenome.models.dna_output.OutputMetadata attribute), [1] SPLICE_SITE_USAGE (alphagenome.models.dna_output.OutputType attribute), [1] splice_sites (alphagenome.models.dna_output.Output attribute), [1] (alphagenome.models.dna_output.OutputMetadata attribute), [1] SPLICE_SITES (alphagenome.models.dna_output.OutputType attribute), [1] SpliceJunctionScorer (class in alphagenome.models.variant_scorers) split() (alphagenome.data.genome.Variant method) SRNA (alphagenome.data.gene_annotation.TranscriptType attribute) STANDARD (alphagenome.visualization.plot_transcripts.TranscriptStylePreset attribute), [1] start (alphagenome.data.genome.Interval attribute), [1] (alphagenome.data.genome.Junction attribute), [1] (alphagenome.data.genome.Variant attribute) start_codon (alphagenome.data.transcript.Transcript attribute), [1] stop_codon (alphagenome.data.transcript.Transcript attribute), [1] strand (alphagenome.data.genome.Interval attribute), [1] (alphagenome.data.genome.Junction attribute), [1] (alphagenome.data.transcript.Transcript attribute), [1] Strand (class in alphagenome.data.genome) strand_int (alphagenome.data.transcript.Transcript attribute), [1] strands (alphagenome.data.track_data.TrackData attribute) Subset (class in alphagenome.data.fold_intervals) swap_strand() (alphagenome.data.genome.Interval method)

T

TEC (alphagenome.data.gene_annotation.TranscriptType attribute) TEST (alphagenome.data.fold_intervals.Subset attribute) tidy_anndata() (in module alphagenome.models.variant_scorers) tidy_scores() (in module alphagenome.models.variant_scorers) to_bytes() (alphagenome.data.genome.Strand method) (alphagenome.data.ontology.OntologyType method) to_dict() (alphagenome.data.genome.Variant method) to_interval_dict() (alphagenome.data.genome.Interval method) to_proto() (alphagenome.data.genome.Interval method) (alphagenome.data.genome.Strand method) (alphagenome.data.genome.Variant method) (alphagenome.data.ontology.OntologyTerm method) (alphagenome.models.dna_client.Organism method) (alphagenome.models.dna_output.OutputType method) (alphagenome.models.variant_scorers.AggregationType method), [1] (alphagenome.models.variant_scorers.CenterMaskScorer method), [1] (alphagenome.models.variant_scorers.ContactMapScorer method), [1] (alphagenome.models.variant_scorers.GeneMaskActiveScorer method), [1] (alphagenome.models.variant_scorers.GeneMaskLFCScorer method), [1] (alphagenome.models.variant_scorers.GeneMaskSplicingScorer method), [1] (alphagenome.models.variant_scorers.PolyadenylationScorer method), [1] (alphagenome.models.variant_scorers.SpliceJunctionScorer method), [1] to_protos() (alphagenome.data.track_data.TrackData method) to_pyranges_dict() (alphagenome.data.genome.Interval method) total_height (alphagenome.visualization.plot_components.AbstractComponent attribute) (alphagenome.visualization.plot_components.ContactMaps attribute) (alphagenome.visualization.plot_components.ContactMapsDiff attribute) (alphagenome.visualization.plot_components.EmptyComponent attribute) (alphagenome.visualization.plot_components.OverlaidTracks attribute) (alphagenome.visualization.plot_components.Sashimi attribute) (alphagenome.visualization.plot_components.SeqLogo attribute) (alphagenome.visualization.plot_components.Tracks attribute) (alphagenome.visualization.plot_components.TranscriptAnnotation attribute)

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) 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), [1] transcript_interval (alphagenome.data.transcript.Transcript attribute), [1] 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) type (alphagenome.data.ontology.OntologyTerm attribute), [1]

U

UBERON (alphagenome.data.ontology.OntologyType attribute) uniprot_id (alphagenome.data.transcript.Transcript attribute), [1] UNITARY_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) UNPROCESSED_PSEUDOGENE (alphagenome.data.gene_annotation.TranscriptType attribute) uns (alphagenome.data.track_data.TrackData attribute), [1] UNSTRANDED (alphagenome.data.genome.Strand attribute)

upsample() (alphagenome.data.track_data.TrackData method) use_default_labels (alphagenome.visualization.plot_components.AbstractAnnotation attribute) utr3 (alphagenome.data.transcript.Transcript attribute), [1] utr3_color (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute), [1] utr5 (alphagenome.data.transcript.Transcript attribute), [1] utr5_color (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute), [1] utr_height (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute), [1]

V

VALID (alphagenome.data.fold_intervals.Subset attribute) validate_sequence_length() (in module alphagenome.models.dna_client) values (alphagenome.data.track_data.TrackData attribute), [1]

Variant (class in alphagenome.data.genome) VariantAnnotation (class in alphagenome.visualization.plot_components) VariantOutput (class in alphagenome.models.dna_output) VAULT_RNA (alphagenome.data.gene_annotation.TranscriptType attribute)

W

width (alphagenome.data.genome.Interval attribute), [1] (alphagenome.data.genome.Junction attribute) (alphagenome.data.track_data.TrackData attribute) (alphagenome.models.variant_scorers.CenterMaskScorer attribute), [1] (alphagenome.models.variant_scorers.GeneMaskSplicingScorer attribute), [1]

within_reference() (alphagenome.data.genome.Interval method)

X

xlim_pad (alphagenome.visualization.plot_transcripts.TranscriptStyle attribute), [1]