Index

A

add() (gene_calling_benchmark.eval.evaluate_predictors.StreamingBenchmark method) AnnotationMode (class in gene_calling_benchmark.label_definition)

as_tuple() (gene_calling_benchmark.LoadedDataset method) available_scopes() (gene_calling_benchmark.label_definition.LabelConfig method)

B

base_overlap (gene_calling_benchmark.transcript_mapping.PredictionMatch attribute) benchmark_from_arrays() (in module gene_calling_benchmark.eval.evaluate_predictors) benchmark_from_gff() (in module gene_calling_benchmark.pipeline)

BenchmarkScope (class in gene_calling_benchmark.label_definition) BEST_PER_LOCUS (gene_calling_benchmark.transcript_mapping.LocusMatchingMode attribute) build_paired_arrays() (in module gene_calling_benchmark.transcript_mapping)

C

clear_benchmark_media_video_buffer() (in module gene_calling_benchmark) compare_multiple_predictions() (in module gene_calling_benchmark.plotting.summary_stat_plotting) compute_global_metrics() (in module gene_calling_benchmark.eval.global_metrics)

compute_overlap_keepsets() (in module gene_calling_benchmark.eval.global_metrics) CONTAINED (gene_calling_benchmark.transcript_mapping.MatchClass attribute) CONTAINS (gene_calling_benchmark.transcript_mapping.MatchClass attribute) count (gene_calling_benchmark.eval.evaluate_predictors.StreamingBenchmark property)

D

default_exon_intron() (gene_calling_benchmark.label_definition.LabelConfig class method)

default_utr_cds_intron() (gene_calling_benchmark.label_definition.LabelConfig class method)

E

EvalMetrics (class in gene_calling_benchmark.label_definition) evaluation_labels (gene_calling_benchmark.label_definition.LabelConfig property)

EXACT (gene_calling_benchmark.transcript_mapping.MatchClass attribute) export_mapping_table() (in module gene_calling_benchmark.transcript_mapping)

F

fn_for_predictors (gene_calling_benchmark.transcript_mapping.TranscriptMapping attribute)

FULL_DISCOVERY (gene_calling_benchmark.transcript_mapping.LocusMatchingMode attribute)

G

gene_calling_benchmark.eval.evaluate_predictors module gene_calling_benchmark.eval.global_metrics module gene_calling_benchmark.label_definition module gene_calling_benchmark.pipeline module

gene_calling_benchmark.plotting.summary_stat_plotting module gene_calling_benchmark.transcript_mapping module get_dataset_info() (in module gene_calling_benchmark) gt_id (gene_calling_benchmark.transcript_mapping.TranscriptMapping attribute)

I

init_wandb_with_presets() (in module gene_calling_benchmark)

is_unmatched_prediction (gene_calling_benchmark.transcript_mapping.TranscriptMapping attribute)

J

junction_f1 (gene_calling_benchmark.transcript_mapping.PredictionMatch attribute)

L

LabelConfig (class in gene_calling_benchmark.label_definition) labels (gene_calling_benchmark.label_definition.LabelConfig property) list_datasets() (in module gene_calling_benchmark) load_dataset() (in module gene_calling_benchmark) LoadedDataset (class in gene_calling_benchmark)

LocusMatchingMode (class in gene_calling_benchmark.transcript_mapping) log_benchmark_all_scalars() (in module gene_calling_benchmark) log_benchmark_media() (in module gene_calling_benchmark) log_benchmark_media_videos() (in module gene_calling_benchmark) log_benchmark_scalars() (in module gene_calling_benchmark)

M

map_transcripts() (in module gene_calling_benchmark.transcript_mapping) MatchClass (class in gene_calling_benchmark.transcript_mapping) matched_predictions (gene_calling_benchmark.transcript_mapping.TranscriptMapping attribute) model_config (gene_calling_benchmark.label_definition.LabelConfig attribute) (gene_calling_benchmark.transcript_mapping.PredictionMatch attribute) (gene_calling_benchmark.transcript_mapping.TranscriptMapping attribute)

module gene_calling_benchmark.eval.evaluate_predictors gene_calling_benchmark.eval.global_metrics gene_calling_benchmark.label_definition gene_calling_benchmark.pipeline gene_calling_benchmark.plotting.summary_stat_plotting gene_calling_benchmark.transcript_mapping

N

name_of() (gene_calling_benchmark.label_definition.LabelConfig method)

O

out_of_scope_labels() (gene_calling_benchmark.label_definition.LabelConfig method)

OVERLAPPING (gene_calling_benchmark.transcript_mapping.MatchClass attribute)

P

PredictionMatch (class in gene_calling_benchmark.transcript_mapping)

R

result() (gene_calling_benchmark.eval.evaluate_predictors.StreamingBenchmark method)

S

scope_tokens() (gene_calling_benchmark.label_definition.LabelConfig method) semantic_boundary_label() (in module gene_calling_benchmark.label_definition) SEMANTIC_BOUNDARY_ORDER (in module gene_calling_benchmark.label_definition) seqid (gene_calling_benchmark.transcript_mapping.TranscriptMapping attribute)

SHARED_JUNCTION (gene_calling_benchmark.transcript_mapping.MatchClass attribute) strand (gene_calling_benchmark.transcript_mapping.TranscriptMapping attribute) StreamingBenchmark (class in gene_calling_benchmark.eval.evaluate_predictors) supports_phase_drift (gene_calling_benchmark.label_definition.LabelConfig property)

T

TranscriptMapping (class in gene_calling_benchmark.transcript_mapping)