Index

A

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

CodonISMResult (class in transcriptml.interpret.codon_ism)

compute_codon_ism() (in module transcriptml.interpret.codon_ism) compute_ism() (in module transcriptml.interpret.ism)

D

DatasetBundle (class in transcriptml.data.bundle)

decode_rna_one_hot() (in module transcriptml.data.encoding)

E

encode_rna_sequence() (in module transcriptml.data.encoding) encode_saluki_transcript() (in module transcriptml.data.encoding) encode_sequences() (in module transcriptml.data.encoding) EnsemblePredictor (class in transcriptml.interpret.predictor)

EpistasisResult (class in transcriptml.interpret.epistasis) evaluate_checkpoint() (in module transcriptml.training.evaluation) evaluate_model() (in module transcriptml.training.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.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)

G

get_schema() (in module transcriptml.data.schemas)

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) iter_gtf_records() (in module transcriptml.data.genomics)

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_transcript_features() (in module transcriptml.data.genomics) LossOutput (class in transcriptml.training.losses)

M

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.models.cnn transcriptml.models.legnet transcriptml.models.registry transcriptml.models.reproduce transcriptml.models.saluki transcriptml.plotting.single_nt_ism transcriptml.training.evaluation transcriptml.training.losses transcriptml.training.metrics transcriptml.training.splits transcriptml.training.trainer 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) 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)

P

parse_gtf_attributes() (in module transcriptml.data.genomics) parse_motif() (in module transcriptml.interpret.motifs) pearson_corr() (in module transcriptml.training.metrics) 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)

R

random_split_indices() (in module transcriptml.training.splits) region_matches_motif() (in module transcriptml.interpret.motifs)

RegressionMSELoss (class in transcriptml.training.losses) reset_parameters() (transcriptml.models.reproduce.SalukiExact method) 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) save_bundle() (in module transcriptml.data.bundle) save_bundle_metadata() (in module transcriptml.data.bundle) save_checkpoint() (in module transcriptml.models.registry) 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) SequenceControlConfig (class in transcriptml.data.controls) SequenceControlOperation (class in transcriptml.data.controls) SequenceSchema (class in transcriptml.data.schemas) SmallCNN (class in transcriptml.models.cnn) SmallCNNConfig (class in transcriptml.models.cnn)

T

to_dict() (transcriptml.data.schemas.SequenceSchema method) (transcriptml.models.registry.ModelConfig method) to_kwargs() (transcriptml.models.cnn.SmallCNNConfig method) (transcriptml.models.legnet.LegNetConfig 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) 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.models.cnn module transcriptml.models.legnet module transcriptml.models.registry module transcriptml.models.reproduce module transcriptml.models.saluki module transcriptml.plotting.single_nt_ism module transcriptml.training.evaluation module transcriptml.training.losses module transcriptml.training.metrics module transcriptml.training.splits module transcriptml.training.trainer module transcriptml.workflows.init_run module TranscriptRecord (class in transcriptml.data.genomics)

W

WeightedMSELoss (class in transcriptml.training.losses)

write_saluki_memmap() (in module transcriptml.data.genomics)