Index

A

aggregate_observations() (in module transcriptml.rbpnet.evaluation_metrics) annotation_channels (transcriptml.data.schemas.SequenceSchema property)

apply_sequence_controls_array() (in module transcriptml.data.controls) apply_sequence_controls_to_bundle() (in module transcriptml.data.controls)

B

base_indices_from_ohe() (in module transcriptml.interpret.motifs) BinomialNLLLoss (class in transcriptml.training.losses) build_model() (in module transcriptml.models.registry)

build_mpra_dataset() (in module transcriptml.data.builders) build_saluki_dataset() (in module transcriptml.data.builders) build_saluki_dataset_from_gtf() (in module transcriptml.data.builders) build_training_loss() (in module transcriptml.training.losses)

C

calculate_gc_fraction() (in module transcriptml.rbpnet.windows) calibration_rows() (in module transcriptml.rbpnet.evaluation_metrics) ChromosomeCVPlan (class in transcriptml.workflows.chromosome_cv) ChromosomeCVResolution (class in transcriptml.workflows.chromosome_cv) CodonISMResult (class in transcriptml.interpret.codon_ism)

collate_rbpnet() (in module transcriptml.rbpnet.dataset) compute_codon_ism() (in module transcriptml.interpret.codon_ism) compute_ism() (in module transcriptml.interpret.ism) compute_window_ism() (in module transcriptml.interpret.window_ism) coordinate_to_genome() (transcriptml.rbpnet.experiment.ProcessedECLIPDataset method) create_chromosome_cv_plan() (in module transcriptml.workflows.chromosome_cv)

D

DatasetBundle (class in transcriptml.data.bundle)

decode_rna_one_hot() (in module transcriptml.data.encoding) deduplicate_locus_indices() (in module transcriptml.rbpnet.dataset)

E

encode() (transcriptml.models.rbpnet.RBPNet method) encode_rna_sequence() (in module transcriptml.data.encoding) encode_saluki_transcript() (in module transcriptml.data.encoding) encode_sequences() (in module transcriptml.data.encoding) enrichment_metrics() (in module transcriptml.rbpnet.evaluation_metrics) EnsemblePredictor (class in transcriptml.interpret.predictor) EpistasisResult (class in transcriptml.interpret.epistasis)

evaluate_checkpoint() (in module transcriptml.training.evaluation) evaluate_fold_checkpoints() (in module transcriptml.training.evaluation) evaluate_model() (in module transcriptml.training.evaluation) evaluate_rbpnet_model() (in module transcriptml.rbpnet.training) evaluate_rbpnet_report() (in module transcriptml.rbpnet.evaluation) exon_count (transcriptml.data.genomics.TranscriptFeature property) extract_transcript_records() (in module transcriptml.data.genomics)

F

find_motif_starts() (in module transcriptml.interpret.motifs) fixed_length_sequence() (in module transcriptml.data.encoding) forward() (transcriptml.models.cnn.SmallCNN method) (transcriptml.models.legnet.LegNet method) (transcriptml.models.rbpnet.RBPNet method) (transcriptml.models.reproduce.SalukiExact method) (transcriptml.models.saluki.SalukiLike method)

forward_features() (transcriptml.models.reproduce.SalukiExact method) from_checkpoint() (transcriptml.interpret.predictor.Predictor class method) from_dict() (transcriptml.data.schemas.SequenceSchema class method) (transcriptml.workflows.chromosome_cv.ChromosomeCVPlan class method)

G

generate_window_bounds() (in module transcriptml.rbpnet.windows) generate_window_starts() (in module transcriptml.interpret.window_ism) genome_to_coordinate() (transcriptml.rbpnet.experiment.ProcessedECLIPDataset method) GenomicBlock (class in transcriptml.rbpnet.experiment)

get_genomic_blocks() (transcriptml.rbpnet.experiment.ProcessedECLIPDataset method) get_profiles() (transcriptml.rbpnet.experiment.ProcessedECLIPDataset method) get_schema() (in module transcriptml.data.schemas) group_split_indices() (in module transcriptml.training.splits) GTFRecord (class in transcriptml.data.genomics)

I

infer_valid_length() (in module transcriptml.data.encoding) infer_valid_lengths() (in module transcriptml.data.encoding) init_run() (in module transcriptml.workflows.init_run)

intervals_overlap() (in module transcriptml.interpret.motifs) ISMResult (class in transcriptml.interpret.ism) item_for_shift() (transcriptml.rbpnet.dataset.RBPNetDataset method) iter_gtf_records() (in module transcriptml.data.genomics)

J

jitter_crop_offset() (in module transcriptml.rbpnet.bundle)

L

LegNet (class in transcriptml.models.legnet) LegNetConfig (class in transcriptml.models.legnet) list_models() (in module transcriptml.models.registry) load_bundle() (in module transcriptml.data.bundle) load_checkpoint() (in module transcriptml.models.registry)

load_chromosome_cv_plan() (in module transcriptml.workflows.chromosome_cv) load_rbpnet_bundle() (in module transcriptml.rbpnet.bundle) load_selection_manifest() (in module transcriptml.rbpnet.selection) load_transcript_features() (in module transcriptml.data.genomics) LossOutput (class in transcriptml.training.losses)

M

make_rbpnet_bundle() (in module transcriptml.rbpnet.bundle) max_abs_effect_per_position() (in module transcriptml.interpret.ism) model_default_params() (in module transcriptml.models.registry) ModelConfig (class in transcriptml.models.registry) module transcriptml.data.builders transcriptml.data.bundle transcriptml.data.controls transcriptml.data.encoding transcriptml.data.genomics transcriptml.data.schemas transcriptml.interpret.ablation transcriptml.interpret.codon_ism transcriptml.interpret.context transcriptml.interpret.epistasis transcriptml.interpret.ism transcriptml.interpret.motifs transcriptml.interpret.predictor transcriptml.interpret.region_ablation transcriptml.interpret.window_ism transcriptml.models.cnn transcriptml.models.legnet transcriptml.models.rbpnet transcriptml.models.registry transcriptml.models.reproduce transcriptml.models.saluki transcriptml.plotting.single_nt_ism transcriptml.rbpnet.bundle transcriptml.rbpnet.dataset transcriptml.rbpnet.evaluation transcriptml.rbpnet.evaluation_metrics transcriptml.rbpnet.experiment transcriptml.rbpnet.losses transcriptml.rbpnet.preprocessing transcriptml.rbpnet.selection transcriptml.rbpnet.training transcriptml.rbpnet.windows transcriptml.training.evaluation transcriptml.training.losses transcriptml.training.metrics transcriptml.training.splits transcriptml.training.trainer transcriptml.workflows.chromosome_cv transcriptml.workflows.init_run

motif_ablation() (in module transcriptml.interpret.ablation) motif_context_scan() (in module transcriptml.interpret.context) motif_epistasis() (in module transcriptml.interpret.epistasis) motif_length() (in module transcriptml.interpret.motifs) MotifAblationResult (class in transcriptml.interpret.ablation) MotifContextResult (class in transcriptml.interpret.context) mse() (in module transcriptml.training.metrics) multinomial_nll() (in module transcriptml.rbpnet.losses) mutation_table_writer() (in module transcriptml.interpret.codon_ism)

N

n_base_channels (transcriptml.data.schemas.SequenceSchema property) n_channels (transcriptml.data.schemas.SequenceSchema property)

normalize_sequence_control_config() (in module transcriptml.data.controls) normalize_splits() (in module transcriptml.training.splits) normalized() (transcriptml.interpret.region_ablation.RegionAblationConfig method)

P

parse_gtf_attributes() (in module transcriptml.data.genomics) parse_motif() (in module transcriptml.interpret.motifs) pearson_corr() (in module transcriptml.training.metrics) PipelineConfig (class in transcriptml.rbpnet.preprocessing) plot_single_nt_ism() (in module transcriptml.plotting.single_nt_ism) predefined_split_indices() (in module transcriptml.training.splits) predict() (transcriptml.interpret.predictor.EnsemblePredictor method) (transcriptml.interpret.predictor.Predictor method)

predict_array() (in module transcriptml.training.evaluation) predict_to_csv() (in module transcriptml.training.evaluation) Predictor (class in transcriptml.interpret.predictor) preprocess_eclip() (in module transcriptml.rbpnet.preprocessing) ProcessedECLIPDataset (class in transcriptml.rbpnet.experiment) profile_metrics() (in module transcriptml.rbpnet.evaluation_metrics)

R

random_split_indices() (in module transcriptml.training.splits) RBPNet (class in transcriptml.models.rbpnet) RBPNetBatch (class in transcriptml.rbpnet.dataset) RBPNetBundleConfig (class in transcriptml.rbpnet.bundle) RBPNetConfig (class in transcriptml.models.rbpnet) RBPNetDataset (class in transcriptml.rbpnet.dataset) RBPNetLossConfig (class in transcriptml.rbpnet.losses) RBPNetLossOutput (class in transcriptml.rbpnet.losses) RBPNetObjective (class in transcriptml.rbpnet.losses) RBPNetOutput (class in transcriptml.models.rbpnet) receptive_field (transcriptml.models.rbpnet.RBPNet property) receptive_field_extents (transcriptml.models.rbpnet.RBPNet property) region_ablation() (in module transcriptml.interpret.region_ablation)

region_matches_motif() (in module transcriptml.interpret.motifs) RegionAblationConfig (class in transcriptml.interpret.region_ablation) RegionAblationInstance (class in transcriptml.interpret.region_ablation) RegionAblationResult (class in transcriptml.interpret.region_ablation) RegionRecord (class in transcriptml.rbpnet.experiment) RegressionMSELoss (class in transcriptml.training.losses) replicate_binomial_nll() (in module transcriptml.rbpnet.losses) replicate_ceiling_metrics() (in module transcriptml.rbpnet.evaluation_metrics) replicates_for() (transcriptml.interpret.region_ablation.RegionAblationConfig method) reset_parameters() (transcriptml.models.reproduce.SalukiExact method) resolve_chromosome_cv_plan() (in module transcriptml.workflows.chromosome_cv) resolve_rbpnet_checkpoint_indices() (in module transcriptml.rbpnet.evaluation) reverse_complement() (in module transcriptml.data.genomics)

S

SalukiExact (class in transcriptml.models.reproduce) SalukiExactConfig (class in transcriptml.models.reproduce) SalukiLike (class in transcriptml.models.saluki) SalukiLikeConfig (class in transcriptml.models.saluki) SameLengthConvTranspose1d (class in transcriptml.models.rbpnet) SamePadConv1d (class in transcriptml.models.rbpnet) Sample (class in transcriptml.rbpnet.preprocessing) SampleRecord (class in transcriptml.rbpnet.experiment) save_bundle() (in module transcriptml.data.bundle) save_bundle_metadata() (in module transcriptml.data.bundle) save_checkpoint() (in module transcriptml.models.registry) save_chromosome_cv_plan() (in module transcriptml.workflows.chromosome_cv) save_codon_ism_result() (in module transcriptml.interpret.codon_ism) save_epistasis_result() (in module transcriptml.interpret.epistasis) save_ism_result() (in module transcriptml.interpret.ism)

save_motif_ablation_result() (in module transcriptml.interpret.ablation) save_motif_context_result() (in module transcriptml.interpret.context) save_region_ablation_result() (in module transcriptml.interpret.region_ablation) save_window_ism_result() (in module transcriptml.interpret.window_ism) scan_windows() (in module transcriptml.rbpnet.windows) select_regions() (in module transcriptml.rbpnet.selection) select_representative_examples() (in module transcriptml.rbpnet.evaluation_metrics) SelectionConfig (class in transcriptml.rbpnet.selection) SelectionManifest (class in transcriptml.rbpnet.selection) SequenceControlConfig (class in transcriptml.data.controls) SequenceControlOperation (class in transcriptml.data.controls) SequenceSchema (class in transcriptml.data.schemas) set_epoch() (transcriptml.rbpnet.dataset.RBPNetDataset method) SmallCNN (class in transcriptml.models.cnn) SmallCNNConfig (class in transcriptml.models.cnn) summarize_regions() (in module transcriptml.rbpnet.windows)

T

theoretical_receptive_field() (in module transcriptml.models.rbpnet) to() (transcriptml.rbpnet.dataset.RBPNetBatch method) to_dict() (transcriptml.data.schemas.SequenceSchema method) (transcriptml.interpret.region_ablation.RegionAblationConfig method) (transcriptml.models.registry.ModelConfig method) (transcriptml.workflows.chromosome_cv.ChromosomeCVPlan method) to_kwargs() (transcriptml.models.cnn.SmallCNNConfig method) (transcriptml.models.legnet.LegNetConfig method) (transcriptml.models.rbpnet.RBPNetConfig method) (transcriptml.models.reproduce.SalukiExactConfig method) (transcriptml.models.saluki.SalukiLikeConfig method) train_from_config() (in module transcriptml.training.trainer) train_model() (in module transcriptml.training.trainer) train_rbpnet_model() (in module transcriptml.rbpnet.training) TrainConfig (class in transcriptml.training.trainer) TrainingLoss (class in transcriptml.training.losses) transcript_length (transcriptml.data.genomics.TranscriptFeature property) TranscriptFeature (class in transcriptml.data.genomics) transcriptml.data.builders module transcriptml.data.bundle module transcriptml.data.controls module transcriptml.data.encoding module transcriptml.data.genomics module transcriptml.data.schemas module transcriptml.interpret.ablation module transcriptml.interpret.codon_ism module transcriptml.interpret.context module transcriptml.interpret.epistasis module transcriptml.interpret.ism module transcriptml.interpret.motifs module transcriptml.interpret.predictor module transcriptml.interpret.region_ablation module transcriptml.interpret.window_ism module transcriptml.models.cnn module

transcriptml.models.legnet module transcriptml.models.rbpnet module transcriptml.models.registry module transcriptml.models.reproduce module transcriptml.models.saluki module transcriptml.plotting.single_nt_ism module transcriptml.rbpnet.bundle module transcriptml.rbpnet.dataset module transcriptml.rbpnet.evaluation module transcriptml.rbpnet.evaluation_metrics module transcriptml.rbpnet.experiment module transcriptml.rbpnet.losses module transcriptml.rbpnet.preprocessing module transcriptml.rbpnet.selection module transcriptml.rbpnet.training module transcriptml.rbpnet.windows module transcriptml.training.evaluation module transcriptml.training.losses module transcriptml.training.metrics module transcriptml.training.splits module transcriptml.training.trainer module transcriptml.workflows.chromosome_cv module transcriptml.workflows.init_run module TranscriptRecord (class in transcriptml.data.genomics) (class in transcriptml.rbpnet.experiment)

V

validate_group_disjoint() (in module transcriptml.training.splits)

W

WeightedMSELoss (class in transcriptml.training.losses) WindowISMResult (class in transcriptml.interpret.window_ism)

WindowScanConfig (class in transcriptml.rbpnet.windows) write_rbpnet_predictions() (in module transcriptml.rbpnet.training) write_saluki_memmap() (in module transcriptml.data.genomics)