Index

A

add_metric() (selene_sdk.utils.PerformanceMetrics method)

AnalyzeSequences (class in selene_sdk.predict)

B

BASE_MODES (selene_sdk.samplers.Sampler attribute) BASE_TO_INDEX (selene_sdk.sequences.Genome attribute) (selene_sdk.sequences.Proteome attribute) (selene_sdk.sequences.Sequence property)

BASES_ARR (selene_sdk.sequences.Genome attribute) (selene_sdk.sequences.Proteome attribute) (selene_sdk.sequences.Sequence property) BedFileSampler (class in selene_sdk.samplers.file_samplers)

C

COMPLEMENTARY_BASE_DICT (selene_sdk.sequences.Genome attribute) coords_in_bounds() (selene_sdk.sequences.Genome method) (selene_sdk.sequences.Proteome method) (selene_sdk.sequences.Sequence method)

create_test_set() (selene_sdk.TrainModel method)

D

DiffScoreHandler (class in selene_sdk.predict.predict_handlers)

E

encoding_to_sequence() (in module selene_sdk.sequences) (selene_sdk.sequences.Genome class method) (selene_sdk.sequences.Proteome class method) (selene_sdk.sequences.Sequence class method)

evaluate() (selene_sdk.EvaluateModel method) (selene_sdk.TrainModel method) EvaluateModel (class in selene_sdk) execute() (in module selene_sdk.utils)

F

from_file() (selene_sdk.interpret.ISMResult static method)

G

Genome (class in selene_sdk.sequences) GenomicFeatures (class in selene_sdk.targets) get_chr_lens() (selene_sdk.sequences.Genome method) get_chrs() (selene_sdk.sequences.Genome method) get_data() (selene_sdk.samplers.file_samplers.BedFileSampler method) (selene_sdk.samplers.file_samplers.MatFileSampler method) get_data_and_targets() (selene_sdk.samplers.file_samplers.BedFileSampler method) (selene_sdk.samplers.file_samplers.MatFileSampler method) (selene_sdk.samplers.OnlineSampler method) (selene_sdk.samplers.Sampler method) get_dataset_in_batches() (selene_sdk.samplers.OnlineSampler method) get_encoding_from_coords() (selene_sdk.sequences.Genome method) (selene_sdk.sequences.Proteome method) (selene_sdk.sequences.Sequence method) get_encoding_from_coords_check_unk() (selene_sdk.sequences.Genome method) get_feature_data() (selene_sdk.targets.GenomicFeatures method) (selene_sdk.targets.Target method)

get_feature_from_index() (selene_sdk.samplers.OnlineSampler method) (selene_sdk.samplers.Sampler method) get_indices_and_probabilities() (in module selene_sdk.utils) get_predictions() (selene_sdk.predict.AnalyzeSequences method) get_predictions_for_bed_file() (selene_sdk.predict.AnalyzeSequences method) get_predictions_for_fasta_file() (selene_sdk.predict.AnalyzeSequences method) get_prot_lens() (selene_sdk.sequences.Proteome method) get_prots() (selene_sdk.sequences.Proteome method) get_reverse_encoding() (in module selene_sdk.sequences) get_score_matrix_for() (selene_sdk.interpret.ISMResult method) get_sequence_from_coords() (selene_sdk.sequences.Genome method) (selene_sdk.sequences.Proteome method) (selene_sdk.sequences.Sequence method) get_sequence_from_encoding() (selene_sdk.samplers.OnlineSampler method) get_test_set() (selene_sdk.samplers.OnlineSampler method) (selene_sdk.samplers.Sampler method) get_validation_set() (selene_sdk.samplers.OnlineSampler method) (selene_sdk.samplers.Sampler method)

H

handle_batch_predictions() (selene_sdk.predict.predict_handlers.DiffScoreHandler method) (selene_sdk.predict.predict_handlers.LogitScoreHandler method) (selene_sdk.predict.predict_handlers.PredictionsHandler method) (selene_sdk.predict.predict_handlers.WritePredictionsHandler method) (selene_sdk.predict.predict_handlers.WriteRefAltHandler method)

heatmap() (in module selene_sdk.interpret)

I

in_silico_mutagenesis() (selene_sdk.predict.AnalyzeSequences method) in_silico_mutagenesis_from_file() (selene_sdk.predict.AnalyzeSequences method) in_silico_mutagenesis_predict() (selene_sdk.predict.AnalyzeSequences method) INDEX_TO_BASE (selene_sdk.sequences.Genome attribute) (selene_sdk.sequences.Proteome attribute) (selene_sdk.sequences.Sequence property)

initialize_logger() (in module selene_sdk.utils) initialize_model() (in module selene_sdk.utils) instantiate() (in module selene_sdk.utils) IntervalsSampler (class in selene_sdk.samplers) is_positive() (selene_sdk.targets.GenomicFeatures method) ISMResult (class in selene_sdk.interpret)

L

load_features_list() (in module selene_sdk.utils) load_model_from_state_dict() (in module selene_sdk.utils)

load_path() (in module selene_sdk.utils) load_variant_abs_diff_scores() (in module selene_sdk.interpret) LogitScoreHandler (class in selene_sdk.predict.predict_handlers)

M

MatFileSampler (class in selene_sdk.samplers.file_samplers) module selene_sdk selene_sdk.interpret selene_sdk.predict selene_sdk.predict.predict_handlers selene_sdk.samplers selene_sdk.samplers.file_samplers selene_sdk.sequences selene_sdk.targets selene_sdk.utils

MultiFileSampler (class in selene_sdk.samplers)

N

NonStrandSpecific (class in selene_sdk.utils)

O

OnlineSampler (class in selene_sdk.samplers)

ordered_variants_and_indices() (in module selene_sdk.interpret)

P

parse_configs_and_run() (in module selene_sdk.utils) PerformanceMetrics (class in selene_sdk.utils)

PredictionsHandler (class in selene_sdk.predict.predict_handlers) Proteome (class in selene_sdk.sequences)

R

RandomPositionsSampler (class in selene_sdk.samplers) reference_sequence (selene_sdk.interpret.ISMResult property)

remove_metric() (selene_sdk.utils.PerformanceMetrics method) rescale_score_matrix() (in module selene_sdk.interpret)

S

sample() (selene_sdk.samplers.file_samplers.BedFileSampler method) (selene_sdk.samplers.file_samplers.MatFileSampler method) (selene_sdk.samplers.IntervalsSampler method) (selene_sdk.samplers.RandomPositionsSampler method) (selene_sdk.samplers.Sampler method) Sampler (class in selene_sdk.samplers) save_dataset_to_file() (selene_sdk.samplers.OnlineSampler method) (selene_sdk.samplers.Sampler method) selene_sdk module selene_sdk.interpret module selene_sdk.predict module selene_sdk.predict.predict_handlers module selene_sdk.samplers module

selene_sdk.samplers.file_samplers module selene_sdk.sequences module selene_sdk.targets module selene_sdk.utils module Sequence (class in selene_sdk.sequences) sequence_logo() (in module selene_sdk.interpret) sequence_to_encoding() (in module selene_sdk.sequences) (selene_sdk.sequences.Genome class method) (selene_sdk.sequences.Proteome class method) (selene_sdk.sequences.Sequence class method) sequence_type (selene_sdk.interpret.ISMResult property) set_mode() (selene_sdk.samplers.Sampler method) sort_standard_chrs() (in module selene_sdk.interpret) STRAND_SIDES (selene_sdk.samplers.OnlineSampler attribute)

T

Target (class in selene_sdk.targets) train() (selene_sdk.TrainModel method)

train_and_validate() (selene_sdk.TrainModel method) TrainModel (class in selene_sdk)

U

UNK_BASE (selene_sdk.sequences.Genome attribute) (selene_sdk.sequences.Proteome attribute) (selene_sdk.sequences.Sequence property)

update() (selene_sdk.utils.PerformanceMetrics method)

V

validate() (selene_sdk.TrainModel method) variant_diffs_scatter_plot() (in module selene_sdk.interpret) variant_effect_prediction() (selene_sdk.predict.AnalyzeSequences method)

visualize() (selene_sdk.utils.PerformanceMetrics method) visualize_precision_recall_curves() (in module selene_sdk.utils) visualize_roc_curves() (in module selene_sdk.utils)

W

write_feature_scores_to_file() (selene_sdk.utils.PerformanceMetrics method) write_to_file() (selene_sdk.predict.predict_handlers.DiffScoreHandler method) (selene_sdk.predict.predict_handlers.LogitScoreHandler method) (selene_sdk.predict.predict_handlers.PredictionsHandler method) (selene_sdk.predict.predict_handlers.WritePredictionsHandler method) (selene_sdk.predict.predict_handlers.WriteRefAltHandler method)

WritePredictionsHandler (class in selene_sdk.predict.predict_handlers) WriteRefAltHandler (class in selene_sdk.predict.predict_handlers)