Index

A

activate() (in module crested.tl.zoo.utils) add_variable() (crested.tl.metrics.ConcordanceCorrelationCoefficient method) (crested.tl.metrics.PearsonCorrelation method) (crested.tl.metrics.PearsonCorrelationLog method) (crested.tl.metrics.SpearmanCorrelationPerClass method) (crested.tl.metrics.ZeroPenaltyMetric method) add_weight() (crested.tl.metrics.ConcordanceCorrelationCoefficient method) (crested.tl.metrics.PearsonCorrelation method) (crested.tl.metrics.PearsonCorrelationLog method) (crested.tl.metrics.SpearmanCorrelationPerClass method) (crested.tl.metrics.ZeroPenaltyMetric method)

AnnDataLoader (class in crested.tl.data) AnnDataModule (class in crested.tl.data) AnnDataset (class in crested.tl.data) annotation (crested.Genome attribute)

B

bar() (in module crested.pl.region) basenji() (in module crested.tl.zoo)

borzoi() (in module crested.tl.zoo) borzoi_prime() (in module crested.tl.zoo)

C

calculate_mean_expression_per_cell_type() (in module crested.tl.modisco) calculate_nucleotide_distribution() (in module crested.utils) calculate_similarity_matrix() (in module crested.tl.modisco) calculate_tomtom_similarity_per_pattern() (in module crested.tl.modisco) call() (crested.tl.losses.CosineMSELogLoss method) (crested.tl.losses.CosineMSELoss method) (crested.tl.losses.PoissonLoss method) (crested.tl.losses.PoissonMultinomialLoss method) change_regions_width() (in module crested.pp) chrom_sizes (crested.Genome attribute) class_instances() (in module crested.pl.modisco) clustermap() (in module crested.pl.modisco) clustermap_tf_motif() (in module crested.pl.modisco) clustermap_tomtom_similarities() (in module crested.pl.modisco) clustermap_with_pwm_logos() (in module crested.pl.modisco) ConcordanceCorrelationCoefficient (class in crested.tl.metrics) contribution_scores() (in module crested.pl.explain) (in module crested.tl) contribution_scores_specific() (in module crested.tl) conv_block() (in module crested.tl.zoo.utils) conv_block_bs() (in module crested.tl.zoo.utils) CosineMSELogLoss (class in crested.tl.losses) CosineMSELoss (class in crested.tl.losses) count() (crested.tl.TaskConfig method) create_pattern_matrix() (in module crested.tl.modisco) create_pattern_tf_dict() (in module crested.tl.modisco) create_plot() (in module crested.pl) create_tf_ct_matrix() (in module crested.tl.modisco) Crested (class in crested.tl) crested.pl module crested.pl.corr module

crested.pl.design module crested.pl.dist module crested.pl.explain module crested.pl.locus module crested.pl.modisco module crested.pl.qc module crested.pl.region module crested.pp module crested.tl module crested.tl.data module crested.tl.design module crested.tl.losses module crested.tl.metrics module crested.tl.modisco module crested.tl.zoo module crested.tl.zoo.utils module crested.utils module

D

data (crested.tl.data.AnnDataLoader attribute) deeptopic_cnn() (in module crested.tl.zoo) deeptopic_lstm() (in module crested.tl.zoo) default_configs() (in module crested.tl) dense_block() (in module crested.tl.zoo.utils) derive_intermediate_sequences() (in module crested.tl.design) (in module crested.utils) dilated_cnn() (in module crested.tl.zoo) dilated_cnn_decoupled() (in module crested.tl.zoo)

dilated_residual() (in module crested.tl.zoo.utils) dtype (crested.tl.losses.CosineMSELogLoss attribute) (crested.tl.losses.CosineMSELoss attribute) (crested.tl.losses.PoissonLoss attribute) (crested.tl.losses.PoissonMultinomialLoss attribute) (crested.tl.metrics.ConcordanceCorrelationCoefficient attribute) (crested.tl.metrics.PearsonCorrelation attribute) (crested.tl.metrics.PearsonCorrelationLog attribute) (crested.tl.metrics.SpearmanCorrelationPerClass attribute) (crested.tl.metrics.ZeroPenaltyMetric attribute)

E

enformer() (in module crested.tl.zoo) enhancer_design_in_silico_evolution() (in module crested.tl) enhancer_design_motif_insertion() (in module crested.tl)

EnhancerOptimizer (class in crested.tl.design) EnhancerOptimizer() (in module crested.utils) evaluate() (in module crested.tl) extract_layer_embeddings() (in module crested.tl)

F

fasta (crested.Genome attribute) fetch() (crested.Genome method) fetch_sequences() (in module crested.utils) ffn_block_enf() (in module crested.tl.zoo.utils) filter_cutoff() (in module crested.pl.qc) filter_regions_on_specificity() (in module crested.pp) find_pattern() (in module crested.tl.modisco) find_pattern_matches() (in module crested.tl.modisco) fit() (crested.tl.Crested method)

flip_region_strand() (in module crested.utils) from_config() (crested.tl.losses.CosineMSELogLoss class method) (crested.tl.losses.CosineMSELoss class method) (crested.tl.losses.PoissonLoss class method) (crested.tl.losses.PoissonMultinomialLoss class method) (crested.tl.metrics.ConcordanceCorrelationCoefficient class method) (crested.tl.metrics.PearsonCorrelation class method) (crested.tl.metrics.PearsonCorrelationLog class method) (crested.tl.metrics.SpearmanCorrelationPerClass class method) (crested.tl.metrics.ZeroPenaltyMetric class method)

G

generate_html_paths() (in module crested.tl.modisco) generate_nucleotide_sequences() (in module crested.tl.modisco) Genome (class in crested) get_best() (crested.tl.design.EnhancerOptimizer method) get_config() (crested.tl.losses.CosineMSELogLoss method) (crested.tl.losses.CosineMSELoss method) (crested.tl.losses.PoissonLoss method) (crested.tl.losses.PoissonMultinomialLoss method) (crested.tl.metrics.ConcordanceCorrelationCoefficient method) (crested.tl.metrics.PearsonCorrelation method) (crested.tl.metrics.PearsonCorrelationLog method) (crested.tl.metrics.SpearmanCorrelationPerClass method) (crested.tl.metrics.ZeroPenaltyMetric method)

get_dataset() (in module crested) get_model() (in module crested) get_motif_db() (in module crested) get_output() (in module crested.tl.zoo.utils) get_pwms_from_modisco_file() (in module crested.tl.modisco) get_sequence() (crested.tl.data.SequenceLoader method)

H

heatmap() (in module crested.pl.corr) heatmap_self() (in module crested.pl.corr)

histogram() (in module crested.pl.dist) hot_encoding_to_sequence() (in module crested.utils)

I

import_beds() (in module crested) import_bigwigs() (in module crested)

in_silico_evolution() (in module crested.tl.design) index() (crested.tl.TaskConfig method)

L

load_model() (crested.tl.Crested method)

locus_scoring() (in module crested.pl.locus) loss (crested.tl.TaskConfig attribute)

M

match_h5_files_to_classes() (in module crested.tl.modisco) metrics (crested.tl.TaskConfig attribute) mha_block_enf() (in module crested.tl.zoo.utils) modisco_results() (in module crested.pl.modisco) module crested.pl crested.pl.corr crested.pl.design crested.pl.dist crested.pl.explain crested.pl.locus crested.pl.modisco crested.pl.qc crested.pl.region crested.pp crested.tl crested.tl.data crested.tl.design crested.tl.losses crested.tl.metrics crested.tl.modisco crested.tl.zoo crested.tl.zoo.utils crested.utils

motif_insertion() (in module crested.tl.design)

N

name (crested.Genome attribute)

normalization_weights() (in module crested.pl.qc) normalize_peaks() (in module crested.pp)

O

one_hot_encode_sequence() (in module crested.utils)

optimizer (crested.tl.TaskConfig attribute)

P

parse_region() (in module crested.utils) pattern_similarity() (in module crested.tl.modisco) PearsonCorrelation (class in crested.tl.metrics) PearsonCorrelationLog (class in crested.tl.metrics) PoissonLoss (class in crested.tl.losses)

PoissonMultinomialLoss (class in crested.tl.losses) pool() (in module crested.tl.zoo.utils) predict() (in module crested.tl) predict_dataloader (crested.tl.data.AnnDataModule attribute) process_patterns() (in module crested.tl.modisco)

R

read_bigwig_region() (in module crested.utils) read_motif_to_tf_file() (in module crested.tl.modisco) register_genome() (in module crested) render_plot() (in module crested.pl) reset_state() (crested.tl.metrics.ConcordanceCorrelationCoefficient method) (crested.tl.metrics.PearsonCorrelation method) (crested.tl.metrics.PearsonCorrelationLog method) (crested.tl.metrics.SpearmanCorrelationPerClass method) (crested.tl.metrics.ZeroPenaltyMetric method)

result() (crested.tl.metrics.ConcordanceCorrelationCoefficient method) (crested.tl.metrics.PearsonCorrelation method) (crested.tl.metrics.PearsonCorrelationLog method) (crested.tl.metrics.SpearmanCorrelationPerClass method) (crested.tl.metrics.ZeroPenaltyMetric method) reverse_complement() (in module crested.utils)

S

scatter() (in module crested.pl.corr) (in module crested.pl.region) score_gene_locus() (in module crested.tl) selected_instances() (in module crested.pl.modisco) SequenceLoader (class in crested.tl.data) setup() (crested.tl.data.AnnDataModule method) setup_logging() (in module crested.utils) similarity_heatmap() (in module crested.pl.modisco) simple_convnet() (in module crested.tl.zoo) sort_and_filter_cutoff() (in module crested.pl.qc) sort_and_filter_regions_on_specificity() (in module crested.pp) SpearmanCorrelationPerClass (class in crested.tl.metrics) stateless_reset_state() (crested.tl.metrics.ConcordanceCorrelationCoefficient method) (crested.tl.metrics.PearsonCorrelation method) (crested.tl.metrics.PearsonCorrelationLog method) (crested.tl.metrics.SpearmanCorrelationPerClass method) (crested.tl.metrics.ZeroPenaltyMetric method)

stateless_result() (crested.tl.metrics.ConcordanceCorrelationCoefficient method) (crested.tl.metrics.PearsonCorrelation method) (crested.tl.metrics.PearsonCorrelationLog method) (crested.tl.metrics.SpearmanCorrelationPerClass method) (crested.tl.metrics.ZeroPenaltyMetric method) stateless_update_state() (crested.tl.metrics.ConcordanceCorrelationCoefficient method) (crested.tl.metrics.PearsonCorrelation method) (crested.tl.metrics.PearsonCorrelationLog method) (crested.tl.metrics.SpearmanCorrelationPerClass method) (crested.tl.metrics.ZeroPenaltyMetric method) step_contribution_scores() (in module crested.pl.design) step_predictions() (in module crested.pl.design)

T

TaskConfig (class in crested.tl) test() (crested.tl.Crested method) test_dataloader (crested.tl.data.AnnDataModule attribute) tf_expression_per_cell_type() (in module crested.pl.modisco) tfmodisco() (in module crested.tl.modisco)

to_dict() (crested.tl.TaskConfig method) track() (in module crested.pl.locus) train_dataloader (crested.tl.data.AnnDataModule attribute) train_val_test_split() (in module crested.pp) transferlearn() (crested.tl.Crested method)

U

update_state() (crested.tl.metrics.ConcordanceCorrelationCoefficient method) (crested.tl.metrics.PearsonCorrelation method) (crested.tl.metrics.PearsonCorrelationLog method) (crested.tl.metrics.SpearmanCorrelationPerClass method) (crested.tl.metrics.ZeroPenaltyMetric method)

V

val_dataloader (crested.tl.data.AnnDataModule attribute) variables (crested.tl.metrics.ConcordanceCorrelationCoefficient attribute) (crested.tl.metrics.PearsonCorrelation attribute) (crested.tl.metrics.PearsonCorrelationLog attribute) (crested.tl.metrics.SpearmanCorrelationPerClass attribute) (crested.tl.metrics.ZeroPenaltyMetric attribute)

violin() (in module crested.pl.corr)

Z

ZeroPenaltyMetric (class in crested.tl.metrics)