Index

_

__call__() (grelu.data.augment.Augmenter method) (grelu.transforms.label_transforms.LabelTransform method) (grelu.transforms.seq_transforms.MotifScore method) (grelu.transforms.seq_transforms.PatternScore method) __getitem__() (grelu.data.dataset.ISMDataset method) (grelu.data.dataset.LabeledSeqDataset method) (grelu.data.dataset.MotifScanDataset method) (grelu.data.dataset.PatternMarginalizeDataset method) (grelu.data.dataset.SeqDataset method) (grelu.data.dataset.VariantDataset method) (grelu.data.dataset.VariantMarginalizeDataset method) (grelu.lightning.ISMDataset method) (grelu.lightning.LabeledSeqDataset method) (grelu.lightning.MotifScanDataset method) (grelu.lightning.PatternMarginalizeDataset method) (grelu.lightning.VariantDataset method) (grelu.lightning.VariantMarginalizeDataset method) __len__() (grelu.data.augment.Augmenter method) (grelu.data.dataset.ISMDataset method) (grelu.data.dataset.LabeledSeqDataset method) (grelu.data.dataset.MotifScanDataset method) (grelu.data.dataset.PatternMarginalizeDataset method) (grelu.data.dataset.SeqDataset method) (grelu.data.dataset.VariantDataset method) (grelu.data.dataset.VariantMarginalizeDataset method) (grelu.lightning.ISMDataset method) (grelu.lightning.LabeledSeqDataset method) (grelu.lightning.MotifScanDataset method) (grelu.lightning.PatternMarginalizeDataset method) (grelu.lightning.VariantDataset method) (grelu.lightning.VariantMarginalizeDataset method) __update__() (grelu.data.dataset.PatternMarginalizeDataset method) (grelu.data.dataset.VariantMarginalizeDataset method) (grelu.lightning.PatternMarginalizeDataset method) (grelu.lightning.VariantMarginalizeDataset method)

_check_multiclass() (in module grelu.data.utils) _check_wandb() (in module grelu.resources) _collect_preds_and_labels() (in module grelu.visualize) _combine_tasks() (grelu.lightning.LightningModelEnsemble method) _create_task_data() (in module grelu.data.utils) _get_dataset_attrs() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) _get_multipliers() (in module grelu.data.augment) _get_pos_k() (grelu.model.layers.Attention method) _get_random_idxs() (grelu.data.augment.Augmenter method) _load_alleles() (grelu.data.dataset.PatternMarginalizeDataset method) (grelu.data.dataset.VariantDataset method) (grelu.data.dataset.VariantMarginalizeDataset method) (grelu.lightning.PatternMarginalizeDataset method) (grelu.lightning.VariantDataset method) (grelu.lightning.VariantMarginalizeDataset method) _load_labels() (grelu.data.dataset.BigWigSeqDataset method) (grelu.data.dataset.LabeledSeqDataset method) (grelu.lightning.LabeledSeqDataset method) _load_seqs() (grelu.data.dataset.ISMDataset method) (grelu.data.dataset.LabeledSeqDataset method) (grelu.data.dataset.MotifScanDataset method) (grelu.data.dataset.PatternMarginalizeDataset method) (grelu.data.dataset.SeqDataset method) (grelu.data.dataset.VariantDataset method) (grelu.data.dataset.VariantMarginalizeDataset method) (grelu.lightning.ISMDataset method) (grelu.lightning.LabeledSeqDataset method) (grelu.lightning.MotifScanDataset method) (grelu.lightning.PatternMarginalizeDataset method) (grelu.lightning.VariantDataset method) (grelu.lightning.VariantMarginalizeDataset method) _load_tasks() (grelu.data.dataset.LabeledSeqDataset method) (grelu.lightning.LabeledSeqDataset method) _split() (grelu.data.augment.Augmenter method) _split_overall_idx() (in module grelu.data.augment)

A

act (grelu.model.blocks.ChannelTransformBlock attribute) (grelu.model.blocks.ConvBlock attribute) (grelu.model.blocks.LinearBlock attribute) (grelu.model.blocks.Stem attribute) (grelu.model.trunks.borzoi.BorzoiTrunk attribute) (grelu.model.trunks.enformer.EnformerTrunk attribute) (grelu.model.trunks.explainn.ExplaiNNConvBlock attribute) act_func (grelu.lightning.ConvHead attribute) (grelu.model.heads.ConvHead attribute) (grelu.model.heads.MLPHead attribute) Activation (class in grelu.model.layers) AdaptivePool (class in grelu.model.layers) add_highlights() (in module grelu.visualize) add_negatives() (in module grelu.data.preprocess) add_transform() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) Aggregate (class in grelu.transforms.prediction_transforms) ALLOWED_BASES (in module grelu.sequence.format) AnnDataSeqDataset (class in grelu.data.dataset)

artifacts() (in module grelu.resources) Attention (class in grelu.model.layers) attn_dropout (grelu.model.layers.Attention attribute) AUGMENTATION_MULTIPLIER_FUNCS (in module grelu.data.augment) Augmenter (class in grelu.data.augment) augmenter (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.data.dataset.PatternMarginalizeDataset attribute) (grelu.data.dataset.SeqDataset attribute) (grelu.data.dataset.VariantDataset attribute) (grelu.data.dataset.VariantMarginalizeDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) (grelu.lightning.PatternMarginalizeDataset attribute) (grelu.lightning.VariantDataset attribute) (grelu.lightning.VariantMarginalizeDataset attribute) average (grelu.lightning.BestF1 attribute) (grelu.lightning.metrics.BestF1 attribute) (grelu.lightning.metrics.MSE attribute) (grelu.lightning.metrics.PearsonCorrCoef attribute) (grelu.lightning.MSE attribute) (grelu.lightning.PearsonCorrCoef attribute)

B

BASE_TO_INDEX_HASH (in module grelu.sequence.format) BaseModel (class in grelu.model.models) BestF1 (class in grelu.lightning) (class in grelu.lightning.metrics) bg (grelu.data.dataset.PatternMarginalizeDataset attribute) (grelu.data.dataset.VariantMarginalizeDataset attribute) (grelu.lightning.PatternMarginalizeDataset attribute) (grelu.lightning.VariantMarginalizeDataset attribute) BigWigSeqDataset (class in grelu.data.dataset) bin_size (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) blocks (grelu.model.blocks.ConvTower attribute) (grelu.model.blocks.TransformerTower attribute) (grelu.model.blocks.UnetTower attribute) (grelu.model.heads.MLPHead attribute) (grelu.model.trunks.borzoi.BorzoiConvTower attribute) (grelu.model.trunks.ConvTower attribute) (grelu.model.trunks.enformer.EnformerConvTower attribute) (grelu.model.trunks.enformer.EnformerTransformerTower attribute) (grelu.model.trunks.explainn.ExplaiNNTrunk attribute) (grelu.model.trunks.TransformerTower attribute)

BorzoiConvTower (class in grelu.model.trunks.borzoi) BorzoiModel (class in grelu.model.models) BorzoiPretrainedModel (class in grelu.model.models) BorzoiTrunk (class in grelu.model.trunks.borzoi) build_model() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method)

C

change_head() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) channel_transform (grelu.lightning.ConvHead attribute) (grelu.model.blocks.UnetBlock attribute) (grelu.model.heads.ConvHead attribute) channels (grelu.model.trunks.explainn.ExplaiNNTrunk attribute) ChannelTransform (class in grelu.model.layers) ChannelTransformBlock (class in grelu.model.blocks) check_bigwig() (in module grelu.io.bigwig) check_equal_lengths() (in module grelu.sequence.utils) check_fasta() (in module grelu.io.fasta) check_indices() (in module grelu.sequence.format) check_intervals() (in module grelu.sequence.format) check_one_hot() (in module grelu.sequence.format) check_reference() (in module grelu.variant) check_string_dna() (in module grelu.sequence.format) clip_intervals() (in module grelu.data.preprocess) compare_func (grelu.transforms.prediction_transforms.Specificity attribute) compare_func_numpy (grelu.transforms.prediction_transforms.Specificity attribute) compare_motifs() (in module grelu.interpret.motifs) compute() (grelu.lightning.BestF1 method) (grelu.lightning.metrics.BestF1 method) (grelu.lightning.metrics.MSE method) (grelu.lightning.metrics.PearsonCorrCoef method) (grelu.lightning.MSE method) (grelu.lightning.PearsonCorrCoef method) (grelu.transforms.prediction_transforms.Aggregate method) (grelu.transforms.prediction_transforms.Specificity method) configure_optimizers() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) conv (grelu.model.blocks.ChannelTransformBlock attribute) (grelu.model.blocks.ConvBlock attribute) (grelu.model.blocks.Stem attribute) (grelu.model.blocks.UnetBlock attribute) (grelu.model.trunks.explainn.ExplaiNNConvBlock attribute)

conv_tower (grelu.model.trunks.borzoi.BorzoiTrunk attribute) (grelu.model.trunks.ConvGRUTrunk attribute) (grelu.model.trunks.ConvTransformerTrunk attribute) (grelu.model.trunks.ConvTrunk attribute) (grelu.model.trunks.DilatedConvTrunk attribute) (grelu.model.trunks.enformer.EnformerTrunk attribute) ConvBlock (class in grelu.model.blocks) convert_input_type() (in module grelu.sequence.format) ConvGRUModel (class in grelu.model.models) ConvGRUTrunk (class in grelu.model.trunks) ConvHead (class in grelu.lightning) (class in grelu.model.heads) ConvMLPModel (class in grelu.model.models) ConvModel (class in grelu.model.models) ConvTower (class in grelu.model.blocks) (class in grelu.model.trunks) ConvTransformerModel (class in grelu.model.models) ConvTransformerTrunk (class in grelu.model.trunks) ConvTrunk (class in grelu.model.trunks) count_params() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) Crop (class in grelu.model.layers) crop (grelu.model.blocks.ConvTower attribute) (grelu.model.trunks.borzoi.BorzoiTrunk attribute) (grelu.model.trunks.ConvTower attribute) (grelu.model.trunks.enformer.EnformerTrunk attribute) curr_seq_idx (grelu.data.dataset.PatternMarginalizeDataset attribute) (grelu.data.dataset.VariantMarginalizeDataset attribute) (grelu.lightning.PatternMarginalizeDataset attribute) (grelu.lightning.VariantMarginalizeDataset attribute)

D

data_params (grelu.lightning.LightningModel attribute) (grelu.lightning.LightningModelEnsemble attribute) (grelu.resources.LightningModel attribute) datasets() (in module grelu.resources) default_train_params (in module grelu.lightning) DEFAULT_WANDB_ENTITY (in module grelu.resources) DEFAULT_WANDB_HOST (in module grelu.resources) delete() (in module grelu.sequence.mutate) dense1 (grelu.model.blocks.FeedForwardBlock attribute) dense2 (grelu.model.blocks.FeedForwardBlock attribute) depthwise (grelu.model.blocks.SeparableConv attribute) DFSeqDataset (class in grelu.data.dataset) DilatedConvModel (class in grelu.model.models)

DilatedConvTrunk (class in grelu.model.trunks) dinuc_shuffle() (in module grelu.sequence.utils) dist_name (in module grelu) drop_ref (grelu.data.dataset.ISMDataset attribute) (grelu.lightning.ISMDataset attribute) Dropout (class in grelu.model.layers) dropout (grelu.model.blocks.ChannelTransformBlock attribute) (grelu.model.blocks.ConvBlock attribute) (grelu.model.blocks.LinearBlock attribute) (grelu.model.blocks.TransformerBlock attribute) (grelu.model.heads.MLPHead attribute) (grelu.model.trunks.enformer.EnformerTransformerBlock attribute) (grelu.model.trunks.explainn.ExplaiNNConvBlock attribute) dropout_p (grelu.model.layers.FlashAttention attribute)

E

embed_dim (grelu.model.layers.FlashAttention attribute) embed_on_dataset() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) embedding (grelu.model.models.BaseModel attribute) end (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.data.dataset.SeqDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) EnformerConvTower (class in grelu.model.trunks.enformer) EnformerModel (class in grelu.model.models) EnformerPretrainedModel (class in grelu.model.models)

EnformerTransformerBlock (class in grelu.model.trunks.enformer) EnformerTransformerTower (class in grelu.model.trunks.enformer) EnformerTrunk (class in grelu.model.trunks.enformer) eps (grelu.lightning.losses.PoissonMultinomialLoss attribute) (grelu.lightning.PoissonMultinomialLoss attribute) evolve() (in module grelu.design) except_tasks (grelu.transforms.prediction_transforms.Aggregate attribute) ExplaiNNConvBlock (class in grelu.model.trunks.explainn) ExplaiNNModel (class in grelu.model.models) ExplaiNNTrunk (class in grelu.model.trunks.explainn) extend_from_coord() (in module grelu.data.preprocess)

F

FeedForwardBlock (class in grelu.model.blocks) ffn (grelu.model.blocks.GRUBlock attribute) (grelu.model.blocks.TransformerBlock attribute) (grelu.model.trunks.enformer.EnformerTransformerBlock attribute) (grelu.model.trunks.GRUBlock attribute) filter() (grelu.transforms.prediction_transforms.Aggregate method) filter_blacklist() (in module grelu.data.preprocess) filter_cells() (in module grelu.data.preprocess) filter_chrom_ends() (in module grelu.data.preprocess) filter_chromosomes() (in module grelu.data.preprocess) filter_coverage() (in module grelu.data.preprocess) filter_intervals() (in module grelu.data.preprocess) filter_obs() (in module grelu.data.preprocess) filter_overlapping() (in module grelu.data.preprocess) filter_random() (in module grelu.data.preprocess) filter_variants() (in module grelu.variant) filters (grelu.model.trunks.borzoi.BorzoiConvTower attribute) flash_attn_qkvpacked_func (grelu.model.layers.FlashAttention attribute) flash_attn_warn (grelu.model.blocks.TransformerBlock attribute) FlashAttention (class in grelu.model.layers) flatten (grelu.model.trunks.explainn.ExplaiNNConvBlock attribute) format_input() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) forward() (grelu.lightning.ConvHead method) (grelu.lightning.LightningModel method) (grelu.lightning.LightningModelEnsemble method) (grelu.lightning.losses.PoissonMultinomialLoss method) (grelu.lightning.PoissonMultinomialLoss method) (grelu.model.blocks.ChannelTransformBlock method) (grelu.model.blocks.ConvBlock method) (grelu.model.blocks.ConvTower method) (grelu.model.blocks.FeedForwardBlock method) (grelu.model.blocks.GRUBlock method) (grelu.model.blocks.LinearBlock method) (grelu.model.blocks.SeparableConv method) (grelu.model.blocks.Stem method) (grelu.model.blocks.TransformerBlock method) (grelu.model.blocks.TransformerTower method) (grelu.model.blocks.UnetBlock method) (grelu.model.blocks.UnetTower method) (grelu.model.heads.ConvHead method) (grelu.model.heads.MLPHead method) (grelu.model.layers.Activation method) (grelu.model.layers.AdaptivePool method) (grelu.model.layers.Attention method) (grelu.model.layers.ChannelTransform method) (grelu.model.layers.Crop method) (grelu.model.layers.Dropout method) (grelu.model.layers.FlashAttention method) (grelu.model.layers.Norm method) (grelu.model.layers.Pool method) (grelu.model.models.BaseModel method) (grelu.model.trunks.borzoi.BorzoiConvTower method) (grelu.model.trunks.borzoi.BorzoiTrunk method) (grelu.model.trunks.ConvGRUTrunk method) (grelu.model.trunks.ConvTower method) (grelu.model.trunks.ConvTransformerTrunk method) (grelu.model.trunks.ConvTrunk method) (grelu.model.trunks.DilatedConvTrunk method) (grelu.model.trunks.enformer.EnformerConvTower method) (grelu.model.trunks.enformer.EnformerTransformerBlock method) (grelu.model.trunks.enformer.EnformerTransformerTower method) (grelu.model.trunks.enformer.EnformerTrunk method) (grelu.model.trunks.explainn.ExplaiNNConvBlock method) (grelu.model.trunks.explainn.ExplaiNNTrunk method) (grelu.model.trunks.GRUBlock method) (grelu.model.trunks.TransformerTower method) (grelu.resources.LightningModel method) (grelu.transforms.label_transforms.LabelTransform method) (grelu.transforms.prediction_transforms.Aggregate method) (grelu.transforms.prediction_transforms.Specificity method) (grelu.transforms.seq_transforms.MotifScore method) (grelu.transforms.seq_transforms.PatternScore method)

frac_mutated_bases (grelu.data.dataset.VariantDataset attribute) (grelu.lightning.VariantDataset attribute)

G

gc() (in module grelu.sequence.metrics) gc_distribution() (in module grelu.sequence.metrics) generate_random_sequences() (in module grelu.sequence.utils) genome (grelu.data.dataset.ISMDataset attribute) (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.data.dataset.MotifScanDataset attribute) (grelu.data.dataset.PatternMarginalizeDataset attribute) (grelu.data.dataset.SeqDataset attribute) (grelu.data.dataset.VariantDataset attribute) (grelu.data.dataset.VariantMarginalizeDataset attribute) (grelu.lightning.ISMDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) (grelu.lightning.MotifScanDataset attribute) (grelu.lightning.PatternMarginalizeDataset attribute) (grelu.lightning.VariantDataset attribute) (grelu.lightning.VariantMarginalizeDataset attribute) get_aggfunc() (in module grelu.lightning) (in module grelu.utils) get_artifact() (in module grelu.resources) get_attention_scores() (in module grelu.interpret.score) get_attn_scores() (grelu.model.layers.Attention method) get_attributions() (in module grelu.interpret.score) get_blacklist_file() (in module grelu.resources) get_central_mask() (in module grelu.model.position) get_chromosomes() (in module grelu.data.utils) get_compare_func() (in module grelu.lightning) (in module grelu.utils) get_dataset_by_model() (in module grelu.resources) get_exponential_embedding() (in module grelu.model.position) get_gc_matched_intervals() (in module grelu.data.preprocess) get_genome() (in module grelu.io.genome) get_input_type() (in module grelu.sequence.format) get_labels() (grelu.data.dataset.LabeledSeqDataset method) (grelu.lightning.LabeledSeqDataset method) get_lengths() (in module grelu.sequence.utils) get_meme_file_path() (in module grelu.resources) get_model_by_dataset() (in module grelu.resources) get_task_idxs() (grelu.lightning.LightningModel method) (grelu.lightning.LightningModelEnsemble method) (grelu.resources.LightningModel method) get_transform_func() (in module grelu.utils) get_unique_length() (in module grelu.sequence.utils) grelu module grelu.data module grelu.data.augment module grelu.data.dataset module grelu.data.preprocess module grelu.data.utils module grelu.design module grelu.interpret module grelu.interpret.motifs module grelu.interpret.score module grelu.io module grelu.io.bed module

grelu.io.bigwig module grelu.io.fasta module grelu.io.genome module grelu.io.motifs module grelu.lightning module grelu.lightning.losses module grelu.lightning.metrics module grelu.model module grelu.model.blocks module grelu.model.heads module grelu.model.layers module grelu.model.models module grelu.model.position module grelu.model.trunks module grelu.model.trunks.borzoi module grelu.model.trunks.enformer module grelu.model.trunks.explainn module grelu.resources module grelu.sequence module grelu.sequence.format module grelu.sequence.metrics module grelu.sequence.mutate module grelu.sequence.utils module grelu.transforms module grelu.transforms.label_transforms module grelu.transforms.prediction_transforms module grelu.transforms.seq_transforms module grelu.utils module grelu.variant module grelu.visualize module gru (grelu.model.blocks.GRUBlock attribute) (grelu.model.trunks.GRUBlock attribute) gru_tower (grelu.model.trunks.ConvGRUTrunk attribute) GRUBlock (class in grelu.model.blocks) (class in grelu.model.trunks)

H

head (grelu.model.models.BaseModel attribute)

head_dim (grelu.model.layers.FlashAttention attribute) hidden_size (grelu.model.heads.MLPHead attribute)

I

in_channels (grelu.lightning.ConvHead attribute) (grelu.model.heads.ConvHead attribute) (grelu.model.heads.MLPHead attribute) in_len (grelu.model.heads.MLPHead attribute) (grelu.model.layers.Attention attribute) INDEX_TO_BASE_HASH (in module grelu.sequence.format) indices_to_one_hot() (in module grelu.sequence.format) indices_to_strings() (in module grelu.sequence.format) initialize_activation() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) initialize_loss() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method)

initialize_metrics() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) input_coord_to_output_bin() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) input_intervals_to_output_bins() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) input_intervals_to_output_intervals() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) insert() (in module grelu.sequence.mutate) intervals_to_strings() (in module grelu.sequence.format) ISM_predict() (in module grelu.interpret.score) ISMDataset (class in grelu.data.dataset) (class in grelu.lightning)

K

key_len (grelu.model.layers.Attention attribute)

L

label_aggfunc (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) label_len (grelu.data.augment.Augmenter attribute) (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) label_transform (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) label_transform_func (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) LabeledSeqDataset (class in grelu.data.dataset) (class in grelu.lightning) LabelTransform (class in grelu.transforms.label_transforms) layer (grelu.model.layers.Dropout attribute)

ledidi() (in module grelu.design) length_aggfunc (grelu.transforms.prediction_transforms.Aggregate attribute) (grelu.transforms.prediction_transforms.Specificity attribute) length_aggfunc_numpy (grelu.transforms.prediction_transforms.Aggregate attribute) (grelu.transforms.prediction_transforms.Specificity attribute) LightningModel (class in grelu.lightning) (class in grelu.resources) LightningModelEnsemble (class in grelu.lightning) linear (grelu.model.blocks.LinearBlock attribute) LinearBlock (class in grelu.model.blocks) load_model() (in module grelu.resources) log_input (grelu.lightning.losses.PoissonMultinomialLoss attribute) (grelu.lightning.PoissonMultinomialLoss attribute)

M

make_insertion_bigwig() (in module grelu.data.preprocess) make_list() (in module grelu.lightning) (in module grelu.utils) make_predict_loader() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) make_test_loader() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) make_train_loader() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) marginalize_patterns() (in module grelu.interpret.motifs) marginalize_variants() (in module grelu.variant) max_clip (grelu.transforms.label_transforms.LabelTransform attribute) max_label_clip (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) max_motif_len (grelu.data.dataset.MotifScanDataset attribute) (grelu.lightning.MotifScanDataset attribute) max_pair_shift (grelu.data.augment.Augmenter attribute) (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) max_seq_shift (grelu.data.augment.Augmenter attribute) (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.data.dataset.SeqDataset attribute) (grelu.data.dataset.VariantDataset attribute) (grelu.data.dataset.VariantMarginalizeDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) (grelu.lightning.VariantDataset attribute) (grelu.lightning.VariantMarginalizeDataset attribute) max_values (grelu.data.augment.Augmenter attribute) merge_intervals_by_column() (in module grelu.data.preprocess) mha (grelu.model.trunks.enformer.EnformerTransformerBlock attribute) min_clip (grelu.transforms.label_transforms.LabelTransform attribute) min_label_clip (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) MLPHead (class in grelu.model.heads) mode (grelu.data.augment.Augmenter attribute) model_names (grelu.lightning.LightningModelEnsemble attribute) model_params (grelu.lightning.LightningModel attribute) (grelu.lightning.LightningModelEnsemble attribute) (grelu.resources.LightningModel attribute) models (grelu.lightning.LightningModelEnsemble attribute) models() (in module grelu.resources) module grelu grelu.data grelu.data.augment grelu.data.dataset grelu.data.preprocess grelu.data.utils grelu.design grelu.interpret grelu.interpret.motifs grelu.interpret.score grelu.io grelu.io.bed grelu.io.bigwig grelu.io.fasta grelu.io.genome grelu.io.motifs grelu.lightning grelu.lightning.losses grelu.lightning.metrics grelu.model grelu.model.blocks grelu.model.heads grelu.model.layers grelu.model.models grelu.model.position grelu.model.trunks grelu.model.trunks.borzoi grelu.model.trunks.enformer grelu.model.trunks.explainn grelu.resources grelu.sequence grelu.sequence.format grelu.sequence.metrics grelu.sequence.mutate grelu.sequence.utils grelu.transforms grelu.transforms.label_transforms grelu.transforms.prediction_transforms grelu.transforms.seq_transforms grelu.utils grelu.variant grelu.visualize

motifs (grelu.data.dataset.MotifScanDataset attribute) (grelu.lightning.MotifScanDataset attribute) (grelu.transforms.seq_transforms.MotifScore attribute) motifs_to_strings() (in module grelu.interpret.motifs) MotifScanDataset (class in grelu.data.dataset) (class in grelu.lightning) MotifScore (class in grelu.transforms.seq_transforms) MSE (class in grelu.lightning) (class in grelu.lightning.metrics) mutate (grelu.data.augment.Augmenter attribute) mutate() (in module grelu.sequence.mutate)

N

n_alleles (grelu.data.dataset.ISMDataset attribute) (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.data.dataset.MotifScanDataset attribute) (grelu.data.dataset.SeqDataset attribute) (grelu.data.dataset.VariantDataset attribute) (grelu.lightning.ISMDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) (grelu.lightning.MotifScanDataset attribute) (grelu.lightning.VariantDataset attribute) n_augmented (grelu.data.dataset.ISMDataset attribute) (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.data.dataset.MotifScanDataset attribute) (grelu.data.dataset.PatternMarginalizeDataset attribute) (grelu.data.dataset.SeqDataset attribute) (grelu.data.dataset.VariantDataset attribute) (grelu.data.dataset.VariantMarginalizeDataset attribute) (grelu.lightning.ISMDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) (grelu.lightning.MotifScanDataset attribute) (grelu.lightning.PatternMarginalizeDataset attribute) (grelu.lightning.VariantDataset attribute) (grelu.lightning.VariantMarginalizeDataset attribute) n_heads (grelu.model.layers.Attention attribute) (grelu.model.layers.FlashAttention attribute) n_mutated_bases (grelu.data.augment.Augmenter attribute) (grelu.data.dataset.VariantDataset attribute) (grelu.lightning.VariantDataset attribute) n_mutated_seqs (grelu.data.augment.Augmenter attribute) (grelu.data.dataset.VariantDataset attribute) (grelu.lightning.VariantDataset attribute)

n_pos_features (grelu.model.layers.Attention attribute) n_seqs (grelu.data.dataset.ISMDataset attribute) (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.data.dataset.MotifScanDataset attribute) (grelu.data.dataset.SeqDataset attribute) (grelu.data.dataset.VariantDataset attribute) (grelu.lightning.ISMDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) (grelu.lightning.MotifScanDataset attribute) (grelu.lightning.VariantDataset attribute) n_shuffles (grelu.data.dataset.PatternMarginalizeDataset attribute) (grelu.data.dataset.VariantMarginalizeDataset attribute) (grelu.lightning.PatternMarginalizeDataset attribute) (grelu.lightning.VariantMarginalizeDataset attribute) n_tasks (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.lightning.ConvHead attribute) (grelu.lightning.LabeledSeqDataset attribute) (grelu.model.heads.ConvHead attribute) (grelu.model.heads.MLPHead attribute) Norm (class in grelu.model.layers) norm (grelu.lightning.ConvHead attribute) (grelu.model.blocks.LinearBlock attribute) (grelu.model.blocks.TransformerBlock attribute) (grelu.model.heads.ConvHead attribute) (grelu.model.heads.MLPHead attribute) (grelu.model.trunks.enformer.EnformerTransformerBlock attribute) (grelu.model.trunks.explainn.ExplaiNNConvBlock attribute) np_log2fc() (in module grelu.utils) numpy_aggregate() (grelu.transforms.prediction_transforms.Aggregate method)

O

off_thresh (grelu.transforms.prediction_transforms.Specificity attribute) off_transform (grelu.transforms.prediction_transforms.Specificity attribute) off_weight (grelu.transforms.prediction_transforms.Specificity attribute) on_save_checkpoint() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) on_test_epoch_end() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) on_transform (grelu.transforms.prediction_transforms.Specificity attribute) on_validation_epoch_end() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method)

one_hot_to_indices() (in module grelu.sequence.format) one_hot_to_strings() (in module grelu.sequence.format) order (grelu.model.blocks.ChannelTransformBlock attribute) (grelu.model.blocks.ConvBlock attribute) out (grelu.model.layers.FlashAttention attribute) out_channels (grelu.model.blocks.ConvTower attribute) (grelu.model.trunks.ConvTower attribute) output_bin_to_input_coord() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method)

P

pad() (in module grelu.sequence.utils) padded_label_len (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) padded_seq_len (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) parse_devices() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) parse_logger() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) PatternMarginalizeDataset (class in grelu.data.dataset) (class in grelu.lightning) patterns (grelu.transforms.seq_transforms.PatternScore attribute) PatternScore (class in grelu.transforms.seq_transforms) pearson (grelu.lightning.metrics.PearsonCorrCoef attribute) (grelu.lightning.PearsonCorrCoef attribute) PearsonCorrCoef (class in grelu.lightning) (class in grelu.lightning.metrics) plot_attention_matrix() (in module grelu.visualize) plot_attributions() (in module grelu.visualize) plot_binary_preds() (in module grelu.visualize) plot_calibration_curve() (in module grelu.visualize) plot_distribution() (in module grelu.visualize) plot_evolution() (in module grelu.visualize) plot_gc_match() (in module grelu.visualize) plot_ISM() (in module grelu.visualize) plot_motif() (in module grelu.visualize) plot_pred_distribution() (in module grelu.visualize) plot_pred_scatter() (in module grelu.visualize) plot_tracks() (in module grelu.visualize) pointwise (grelu.model.blocks.SeparableConv attribute) pointwise_conv (grelu.model.trunks.borzoi.BorzoiTrunk attribute) (grelu.model.trunks.enformer.EnformerTrunk attribute)

PoissonMultinomialLoss (class in grelu.lightning) (class in grelu.lightning.losses) Pool (class in grelu.model.layers) pool (grelu.lightning.ConvHead attribute) (grelu.model.blocks.ConvBlock attribute) (grelu.model.blocks.Stem attribute) (grelu.model.heads.ConvHead attribute) (grelu.model.trunks.explainn.ExplaiNNConvBlock attribute) pool_factor (grelu.model.blocks.ConvTower attribute) (grelu.model.trunks.ConvTower attribute) pool_func (grelu.lightning.ConvHead attribute) (grelu.model.heads.ConvHead attribute) pos_dropout (grelu.model.layers.Attention attribute) positional_embed (grelu.model.layers.Attention attribute) positions (grelu.data.dataset.ISMDataset attribute) (grelu.data.dataset.MotifScanDataset attribute) (grelu.lightning.ISMDataset attribute) (grelu.lightning.MotifScanDataset attribute) (grelu.transforms.prediction_transforms.Aggregate attribute) predict (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) predict_on_dataset() (grelu.lightning.LightningModel method) (grelu.lightning.LightningModelEnsemble method) (grelu.resources.LightningModel method) predict_on_seqs() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) predict_variant_effects() (in module grelu.variant) products (grelu.data.augment.Augmenter attribute) projects() (in module grelu.resources) protect (grelu.data.augment.Augmenter attribute) pthresh (grelu.transforms.seq_transforms.MotifScore attribute)

Q

qkv (grelu.model.layers.FlashAttention attribute)

R

random_mutate() (in module grelu.sequence.mutate) rc (grelu.data.augment.Augmenter attribute) (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.data.dataset.PatternMarginalizeDataset attribute) (grelu.data.dataset.SeqDataset attribute) (grelu.data.dataset.VariantDataset attribute) (grelu.data.dataset.VariantMarginalizeDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) (grelu.lightning.PatternMarginalizeDataset attribute) (grelu.lightning.VariantDataset attribute) (grelu.lightning.VariantMarginalizeDataset attribute) (grelu.transforms.seq_transforms.MotifScore attribute) RC_HASH (in module grelu.sequence.utils) rc_label() (in module grelu.data.augment) rc_seq() (in module grelu.data.augment) read_bed() (in module grelu.io.bed) read_bigwig() (in module grelu.io.bigwig) read_fasta() (in module grelu.io.fasta) read_gtf() (in module grelu.io.genome) read_meme_file() (in module grelu.io.motifs) read_modisco_report() (in module grelu.io.motifs)

read_narrowpeak() (in module grelu.io.bed) read_sizes() (in module grelu.io.genome) read_tomtom() (in module grelu.io) receptive_field (grelu.model.blocks.ConvTower attribute) (grelu.model.trunks.ConvTower attribute) reduction (grelu.lightning.losses.PoissonMultinomialLoss attribute) (grelu.lightning.PoissonMultinomialLoss attribute) rel_content_bias (grelu.model.layers.Attention attribute) rel_pos_bias (grelu.model.layers.Attention attribute) reset() (grelu.lightning.metrics.PearsonCorrCoef method) (grelu.lightning.PearsonCorrCoef method) reset_transform() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) residual (grelu.model.blocks.ConvBlock attribute) resize() (in module grelu.sequence.utils) return_pre_pool (grelu.model.blocks.ConvBlock attribute) reverse_complement() (in module grelu.sequence.utils) rng (grelu.data.augment.Augmenter attribute) rotary_embed (grelu.model.layers.FlashAttention attribute) run_modisco() (in module grelu.interpret.score) runs() (in module grelu.resources)

S

scan_sequences() (in module grelu.interpret.motifs) sconv (grelu.model.blocks.UnetBlock attribute) seed (grelu.data.dataset.PatternMarginalizeDataset attribute) (grelu.data.dataset.VariantMarginalizeDataset attribute) (grelu.lightning.PatternMarginalizeDataset attribute) (grelu.lightning.VariantMarginalizeDataset attribute) SeparableConv (class in grelu.model.blocks) seq_differences() (in module grelu.sequence.mutate) seq_len (grelu.data.augment.Augmenter attribute) (grelu.data.dataset.ISMDataset attribute) (grelu.data.dataset.LabeledSeqDataset attribute) (grelu.data.dataset.MotifScanDataset attribute) (grelu.data.dataset.PatternMarginalizeDataset attribute) (grelu.data.dataset.SeqDataset attribute) (grelu.data.dataset.VariantDataset attribute) (grelu.data.dataset.VariantMarginalizeDataset attribute) (grelu.lightning.ISMDataset attribute) (grelu.lightning.LabeledSeqDataset attribute) (grelu.lightning.MotifScanDataset attribute) (grelu.lightning.PatternMarginalizeDataset attribute) (grelu.lightning.VariantDataset attribute) (grelu.lightning.VariantMarginalizeDataset attribute)

SeqDataset (class in grelu.data.dataset) shift() (in module grelu.data.augment) shift_label (grelu.data.augment.Augmenter attribute) shift_seq (grelu.data.augment.Augmenter attribute) Specificity (class in grelu.transforms.prediction_transforms) split() (in module grelu.data.preprocess) STANDARD_BASES (in module grelu.sequence.format) Stem (class in grelu.model.blocks) strings_to_indices() (in module grelu.sequence.format) strings_to_one_hot() (in module grelu.lightning) (in module grelu.sequence.format)

T

task_aggfunc (grelu.transforms.prediction_transforms.Aggregate attribute) task_aggfunc_numpy (grelu.transforms.prediction_transforms.Aggregate attribute) tasks (grelu.transforms.prediction_transforms.Aggregate attribute) (grelu.transforms.prediction_transforms.Specificity attribute) test_on_dataset() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) test_step() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) to_k (grelu.model.layers.Attention attribute) to_out (grelu.model.layers.Attention attribute) to_pos_k (grelu.model.layers.Attention attribute) to_q (grelu.model.layers.Attention attribute) to_v (grelu.model.layers.Attention attribute) torch_aggregate() (grelu.transforms.prediction_transforms.Aggregate method) torch_log2fc() (in module grelu.utils) torch_maxval() (in module grelu.utils) torch_minval() (in module grelu.utils) total_weight (grelu.lightning.losses.PoissonMultinomialLoss attribute) (grelu.lightning.PoissonMultinomialLoss attribute)

train_on_dataset() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) train_params (grelu.lightning.LightningModel attribute) (grelu.resources.LightningModel attribute) training_step() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) transform_func (grelu.transforms.label_transforms.LabelTransform attribute) transformer_tower (grelu.model.trunks.borzoi.BorzoiTrunk attribute) (grelu.model.trunks.ConvTransformerTrunk attribute) (grelu.model.trunks.enformer.EnformerTrunk attribute) TransformerBlock (class in grelu.model.blocks) TransformerTower (class in grelu.model.blocks) (class in grelu.model.trunks) trim() (in module grelu.sequence.utils) trim_pwm() (in module grelu.interpret.motifs) tune_on_dataset() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method)

U

unet_tower (grelu.model.trunks.borzoi.BorzoiTrunk attribute) UnetBlock (class in grelu.model.blocks) UnetTower (class in grelu.model.blocks) update() (grelu.lightning.BestF1 method) (grelu.lightning.metrics.BestF1 method) (grelu.lightning.metrics.MSE method) (grelu.lightning.metrics.PearsonCorrCoef method) (grelu.lightning.MSE method) (grelu.lightning.PearsonCorrCoef method)

update_ckpt() (in module grelu.io) update_metrics() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) upsample (grelu.model.blocks.UnetBlock attribute)

V

validation_step() (grelu.lightning.LightningModel method) (grelu.resources.LightningModel method) value_len (grelu.model.layers.Attention attribute) variant_to_seqs() (in module grelu.variant)

VariantDataset (class in grelu.data.dataset) (class in grelu.lightning) VariantMarginalizeDataset (class in grelu.data.dataset) (class in grelu.lightning) variants_to_intervals() (in module grelu.variant)

W

weight_off() (grelu.transforms.prediction_transforms.Specificity method)

weights (grelu.transforms.seq_transforms.PatternScore attribute)