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AlphaGenome
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Installation
Getting started
Tutorials
Choosing a condition
Selecting a genomic region
Predicting tracks for an interval or sequence
Predicting a variant
Scoring a variant
Plotting predictions
Conditioning on your own single-cell data
Working with imputed tracks
Analyzing a splicing variant
Analyzing haplotypes
Highlighting important regions with ISM
Making mouse predictions
AlphaGenome 1 quick start (legacy)
Deriving PSI values from splice junctions
User guide
Key objects
Model output metadata
Navigating imputed tracks
How variant scoring works
Visualization basics
Migrating from AlphaGenome 1
Vignettes
Fine-mapping the
ETS2
locus
Dissecting non-coding
TAL1
mutations in T-ALL
Mapping lineage-specific enhancers at the
BCL11A
locus
API reference
Models
AlphaGenome 2
create
ModelVersion
Organism
validate_sequence_length
DnaClient
encode_cells
observed_metadata
predict_interval
predict_interval_gradients
predict_interval_gradients_batch
predict_intervals
predict_sequence
predict_sequences
predict_variant
predict_variants
score_interval
score_intervals
score_ism_variants
score_variant
score_variants
supported_conditions
OutputType
Output
filter_output_type
filter_to_observed
filter_to_strand
get
map_over_outputs
resize
with_metadata_column
with_name_suffix
OutputMetadata
concatenate
get
VariantOutput
TargetGeneMetadata
InputGradientsOutput
to_track_data
ModelCondition
from_curies
from_anndata
subsample
AggregationType
BaseVariantScorer
CenterMaskScorer
ContactMapScorer
GeneMaskLFCScorer
GeneMaskActiveScorer
GeneMaskSplicingScorer
MethylationScorer
PolyadenylationScorer
SpliceJunctionScorer
get_recommended_scorers
tidy_anndata
tidy_scores
IntervalAggregationType
BaseIntervalScorer
GeneMaskScorer
AlphaGenome 1
create
ModelVersion
Organism
validate_sequence_length
DnaClient
output_metadata
predict_interval
predict_intervals
predict_sequence
predict_sequences
predict_variant
predict_variants
score_interval
score_intervals
score_ism_variants
score_variant
score_variants
OutputType
Output
filter_ontology_terms
filter_output_type
filter_to_strand
get
map_track_data
resize
OutputMetadata
concatenate
from_outputs
get
VariantOutput
AggregationType
BaseVariantScorer
CenterMaskScorer
ContactMapScorer
GeneMaskLFCScorer
GeneMaskActiveScorer
GeneMaskSplicingScorer
PolyadenylationScorer
SpliceJunctionScorer
get_recommended_scorers
tidy_anndata
tidy_scores
IntervalAggregationType
BaseIntervalScorer
GeneMaskScorer
get_api_key
Atlas
create
AtlasClient
query_interval
query_variant
query_variants
scorer_metadata
ScorerMetadata
Data
Subset
get_all_folds
get_fold_names
get_fold_intervals
Strand
from_str
VariantFormat
to_regex
Interval
as_unstranded
binary_mask
binary_mask_stranded
boundary_shift
center
contains
copy
coverage
coverage_stranded
from_interval_dict
from_str
intersect
overlap_ranges
overlaps
pad
resize
shift
swap_strand
to_interval_dict
truncate
within_reference
Variant
alternate_overlaps
as_truncated_str
copy
from_dict
from_str
reference_overlaps
split
to_dict
Junction
acceptor_region
as_unstranded
binary_mask
binary_mask_stranded
boundary_shift
center
contains
copy
coverage
coverage_stranded
dinucleotide_region
donor_region
from_interval_dict
from_str
intersect
overlap_ranges
overlaps
pad
resize
shift
swap_strand
to_interval_dict
truncate
within_reference
normalize_variant
intersect_intervals
merge_overlapping_intervals
union_intervals
TranscriptType
extract_tss
filter_transcript_type
filter_protein_coding
filter_to_longest_transcript
filter_to_mane_select_transcript
filter_transcript_support_level
get_gene_interval
get_gene_intervals
FastaExtractor
extract
get_length_for_sequence_name
reverse_complement
JunctionData
filter_by_name
filter_by_ontology
filter_by_tissue
filter_to_negative_strand
filter_to_observed
filter_to_positive_strand
filter_to_strand
filter_tracks
intersect_with_interval
normalize_values
with_metadata_column
with_name_suffix
get_junctions_to_plot
OntologyType
OntologyTerm
from_curie
from_curies
AggregationType
TrackData
bin_index
change_resolution
copy
downsample
filter_to_negative_strand
filter_to_nonnegative_strand
filter_to_nonpositive_strand
filter_to_observed
filter_to_positive_strand
filter_to_stranded
filter_to_unstranded
filter_tracks
groupby
pad
resize
reverse_complement
select_tracks_by_index
select_tracks_by_name
slice_by_interval
slice_by_positions
upsample
with_metadata_column
with_name_suffix
concat
interleave
GeneExpressionData
copy
filter_to_negative_strand
filter_to_nonnegative_strand
filter_to_nonpositive_strand
filter_to_observed
filter_to_positive_strand
filter_to_protein_coding
filter_to_stranded
filter_to_unstranded
filter_tracks
get_genes_as_intervals
resize
select_tracks_by_index
slice_by_interval
to_anndata
with_metadata_column
with_name_suffix
concat
Transcript
fix_truncation
from_gtf_df
offset_in_cds
TranscriptExtractor
cache_transcripts
extract
Interpretation
ism_variants
ism_matrix
tile_interval
score_enhancers
get_active_enhancers
assign_consensus_enhancers
Visualization
seqlogo
plot_contact_map
plot_track
plot_tracks
sashimi_plot
enhancer_arcs_plot
pad_track
plot
AbstractComponent
get_ax_height
plot_ax
Tracks
get_ax_height
plot_ax
OverlaidTracks
get_ax_height
plot_ax
ContactMaps
get_ax_height
plot_ax
ContactMapsDiff
get_ax_height
plot_ax
GeneExpression
get_ax_height
plot_ax
OverlaidGeneExpression
get_ax_height
plot_ax
TranscriptAnnotation
get_ax_height
plot_ax
SeqLogo
get_ax_height
plot_ax
Sashimi
get_ax_height
plot_ax
FeatureContribution
get_ax_height
plot_ax
ScoreBar
get_ax_height
plot_ax
EnhancerArcs
get_ax_height
plot_ax
EmptyComponent
get_ax_height
plot_ax
AbstractAnnotation
add_label
plot_ax
plot_labels
IntervalAnnotation
add_label
plot_ax
plot_labels
VariantAnnotation
add_label
plot_ax
plot_labels
TranscriptStyle
TranscriptStylePreset
plot_transcripts
draw_interval
draw_transcript
FAQs
Resources
References
Community
.rst
.pdf
System Settings
Light
Dark
copy
Contents
TrackData.copy()
copy
#
TrackData.
copy
(
)
[source]
#
Returns a deep copy of the
TrackData
object.
Return type
:
TrackData
Contents
TrackData.copy()