Index

_

__getitem__() (scooby.data.onTheFlyDataset method) (scooby.data.onTheFlyMultiomeDataset method) (scooby.data.onTheFlyPseudobulkDataset method) (scooby.data.scdata.onTheFlyDataset method) (scooby.data.scdata.onTheFlyMultiomeDataset method) (scooby.data.scdata.onTheFlyPseudobulkDataset method) __len__() (scooby.data.onTheFlyDataset method) (scooby.data.onTheFlyMultiomeDataset method) (scooby.data.onTheFlyPseudobulkDataset method) (scooby.data.scdata.onTheFlyDataset method) (scooby.data.scdata.onTheFlyMultiomeDataset method) (scooby.data.scdata.onTheFlyPseudobulkDataset method) _get_neighbors_for_cell() (scooby.data.onTheFlyDataset method) (scooby.data.onTheFlyMultiomeDataset method) (scooby.data.scdata.onTheFlyDataset method) (scooby.data.scdata.onTheFlyMultiomeDataset method) _init_weights() (scooby.modeling.Scooby method) (scooby.modeling.scooby.Scooby method) _load_pseudobulk() (scooby.data.onTheFlyDataset method) (scooby.data.onTheFlyMultiomeDataset method) (scooby.data.onTheFlyPseudobulkDataset method) (scooby.data.scdata.onTheFlyDataset method) (scooby.data.scdata.onTheFlyMultiomeDataset method) (scooby.data.scdata.onTheFlyPseudobulkDataset method)

_process_atac() (scooby.data.onTheFlyMultiomeDataset method) (scooby.data.scdata.onTheFlyMultiomeDataset method) _process_cells() (scooby.data.onTheFlyDataset method) (scooby.data.scdata.onTheFlyDataset method) _process_paths() (scooby.data.onTheFlyPseudobulkDataset method) (scooby.data.scdata.onTheFlyPseudobulkDataset method) _process_rna() (scooby.data.onTheFlyMultiomeDataset method) (scooby.data.scdata.onTheFlyMultiomeDataset method) _reinit_fasta_reader() (scooby.data.onTheFlyDataset method) (scooby.data.onTheFlyMultiomeDataset method) (scooby.data.onTheFlyPseudobulkDataset method) (scooby.data.scdata.onTheFlyDataset method) (scooby.data.scdata.onTheFlyMultiomeDataset method) (scooby.data.scdata.onTheFlyPseudobulkDataset method) _sparse_to_coverage_atac() (in module scooby.data) (in module scooby.data.scdata) _sparse_to_coverage_rna() (in module scooby.data) (in module scooby.data.scdata)

A

adata_minus (scooby.data.onTheFlyDataset attribute) (scooby.data.scdata.onTheFlyDataset attribute) adata_plus (scooby.data.onTheFlyDataset attribute) (scooby.data.scdata.onTheFlyDataset attribute)

adatas (scooby.data.onTheFlyMultiomeDataset attribute) (scooby.data.scdata.onTheFlyMultiomeDataset attribute) add_exon() (scooby.utils.transcriptome.Gene method) add_heatmap_to_axes() (in module scooby.utils.plotting) add_weight_decay() (in module scooby.utils.utils)

B

base_path (scooby.data.onTheFlyPseudobulkDataset attribute) (scooby.data.scdata.onTheFlyPseudobulkDataset attribute)

batch_conv (in module scooby.modeling.scooby) bedtool_exon() (scooby.utils.transcriptome.Transcriptome method) bedtool_span() (scooby.utils.transcriptome.Transcriptome method)

C

cachesize (scooby.modeling.Scooby attribute) (scooby.modeling.scooby.Scooby attribute) cell_emb_dim (scooby.modeling.Scooby attribute) (scooby.modeling.scooby.Scooby attribute) cell_sample_size (scooby.data.onTheFlyDataset attribute) (scooby.data.onTheFlyMultiomeDataset attribute) (scooby.data.scdata.onTheFlyDataset attribute) (scooby.data.scdata.onTheFlyMultiomeDataset attribute) cell_state_to_conv (scooby.modeling.Scooby attribute) (scooby.modeling.scooby.Scooby attribute) cell_types (scooby.data.onTheFlyPseudobulkDataset attribute) (scooby.data.scdata.onTheFlyPseudobulkDataset attribute) cell_weights (scooby.data.onTheFlyDataset attribute) (scooby.data.onTheFlyMultiomeDataset attribute) (scooby.data.scdata.onTheFlyDataset attribute) (scooby.data.scdata.onTheFlyMultiomeDataset attribute)

cells_to_run (scooby.data.onTheFlyDataset attribute) (scooby.data.onTheFlyMultiomeDataset attribute) (scooby.data.scdata.onTheFlyDataset attribute) (scooby.data.scdata.onTheFlyMultiomeDataset attribute) chrom (scooby.utils.transcriptome.Gene attribute) clip_soft (scooby.data.onTheFlyDataset attribute) (scooby.data.onTheFlyMultiomeDataset attribute) (scooby.data.onTheFlyPseudobulkDataset attribute) (scooby.data.scdata.onTheFlyDataset attribute) (scooby.data.scdata.onTheFlyMultiomeDataset attribute) (scooby.data.scdata.onTheFlyPseudobulkDataset attribute) custom_read_length (scooby.data.onTheFlyDataset attribute) (scooby.data.onTheFlyMultiomeDataset attribute) (scooby.data.onTheFlyPseudobulkDataset attribute) (scooby.data.scdata.onTheFlyDataset attribute) (scooby.data.scdata.onTheFlyMultiomeDataset attribute) (scooby.data.scdata.onTheFlyPseudobulkDataset attribute)

D

disable_cache (scooby.modeling.Scooby attribute) (scooby.modeling.scooby.Scooby attribute)

dna_letter_at() (in module scooby.utils.utils)

E

embedding (scooby.data.onTheFlyDataset attribute) (scooby.data.onTheFlyMultiomeDataset attribute) (scooby.data.scdata.onTheFlyDataset attribute) (scooby.data.scdata.onTheFlyMultiomeDataset attribute)

embedding_dim (scooby.modeling.Scooby attribute) (scooby.modeling.scooby.Scooby attribute) evaluate() (in module scooby.utils.utils) exons (scooby.utils.transcriptome.Gene attribute)

F

fix_rev_comp_multiome() (in module scooby.utils.utils) fix_rev_comp_rna() (in module scooby.utils.utils) forward() (scooby.modeling.Scooby method) (scooby.modeling.scooby.Scooby method) forward_cell_embs_only() (scooby.modeling.Scooby method) (scooby.modeling.scooby.Scooby method)

forward_convs_on_emb() (scooby.modeling.Scooby method) (scooby.modeling.scooby.Scooby method) forward_seq_to_emb() (scooby.modeling.Scooby method) (scooby.modeling.scooby.Scooby method) forward_sequence_w_convs() (scooby.modeling.Scooby method) (scooby.modeling.scooby.Scooby method)

G

Gene (class in scooby.utils.transcriptome) genes (scooby.utils.transcriptome.Transcriptome attribute) genome_ds (scooby.data.onTheFlyDataset attribute) (scooby.data.onTheFlyMultiomeDataset attribute) (scooby.data.onTheFlyPseudobulkDataset attribute) (scooby.data.scdata.onTheFlyDataset attribute) (scooby.data.scdata.onTheFlyMultiomeDataset attribute) (scooby.data.scdata.onTheFlyPseudobulkDataset attribute) get_cell_count_pred() (in module scooby.utils.utils) get_cell_profile_pred() (in module scooby.utils.utils) get_exons() (scooby.utils.transcriptome.Gene method)

get_gene_slice_and_strand() (in module scooby.utils.utils) get_lora() (in module scooby.utils.utils) get_outputs() (in module scooby.utils.utils) get_pseudobulk_count_pred() (in module scooby.utils.utils) get_pseudobulk_profile_pred() (in module scooby.utils.utils) get_targets (scooby.data.onTheFlyDataset attribute) (scooby.data.onTheFlyMultiomeDataset attribute) (scooby.data.scdata.onTheFlyDataset attribute) (scooby.data.scdata.onTheFlyMultiomeDataset attribute) get_targets() (in module scooby.utils.utils) gtf_kv() (in module scooby.utils.transcriptome)

K

kv (scooby.utils.transcriptome.Gene attribute)

M

max_value (in module scooby.data) (in module scooby.data.scdata) midpoint() (scooby.utils.transcriptome.Gene method) min_value (in module scooby.data) (in module scooby.data.scdata) module scooby scooby.data scooby.data.scdata scooby.modeling scooby.modeling.scooby scooby.utils scooby.utils.plotting scooby.utils.transcriptome scooby.utils.utils

multinomial_torch() (in module scooby.utils.utils)

N

n_tracks (scooby.modeling.Scooby attribute) (scooby.modeling.scooby.Scooby attribute) neighbors (scooby.data.onTheFlyDataset attribute) (scooby.data.onTheFlyMultiomeDataset attribute) (scooby.data.scdata.onTheFlyDataset attribute) (scooby.data.scdata.onTheFlyMultiomeDataset attribute)

normalize_atac (scooby.data.onTheFlyMultiomeDataset attribute) (scooby.data.scdata.onTheFlyMultiomeDataset attribute)

O

onTheFlyDataset (class in scooby.data) (class in scooby.data.scdata) onTheFlyMultiomeDataset (class in scooby.data) (class in scooby.data.scdata)

onTheFlyPseudobulkDataset (class in scooby.data) (class in scooby.data.scdata) output_slice() (scooby.utils.transcriptome.Gene method)

P

plot_bed() (in module scooby.utils.plotting) plot_coverage() (in module scooby.utils.plotting) plot_line() (in module scooby.utils.plotting) plot_seq_scores() (in module scooby.utils.utils)

plot_tracks() (in module scooby.utils.plotting) poisson_multinomial_torch() (in module scooby.utils.utils) poisson_torch() (in module scooby.utils.utils) process_atac() (in module scooby.utils.utils) process_rna() (in module scooby.utils.utils)

R

random_cells (scooby.data.onTheFlyDataset attribute) (scooby.data.onTheFlyMultiomeDataset attribute) (scooby.data.scdata.onTheFlyDataset attribute) (scooby.data.scdata.onTheFlyMultiomeDataset attribute)

read_backed() (in module scooby.utils.utils) read_gtf() (scooby.utils.transcriptome.Transcriptome method) region_to_bin() (in module scooby.utils.utils)

S

scooby module Scooby (class in scooby.modeling) (class in scooby.modeling.scooby) scooby.data module scooby.data.scdata module scooby.modeling module scooby.modeling.scooby module

scooby.utils module scooby.utils.plotting module scooby.utils.transcriptome module scooby.utils.utils module seqlevelstyle (scooby.data.onTheFlyPseudobulkDataset attribute) (scooby.data.scdata.onTheFlyPseudobulkDataset attribute) span() (scooby.utils.transcriptome.Gene method) squashed_scale() (in module scooby.utils.utils) strand (scooby.utils.transcriptome.Gene attribute)

T

Transcriptome (class in scooby.utils.transcriptome)

U

undo_squashed_scale() (in module scooby.utils.utils) use_geneid (scooby.utils.transcriptome.Transcriptome attribute)

use_transform_borzoi_emb (scooby.modeling.Scooby attribute) (scooby.modeling.scooby.Scooby attribute)

V

visualize_input_gradient_pair() (in module scooby.utils.utils)

W

write_bed_exon() (scooby.utils.transcriptome.Transcriptome method)

write_bed_span() (scooby.utils.transcriptome.Transcriptome method)