Index

A

add_layernorm (DeSCOPEModelArguments attribute) all_anndata_pair_metrics (CellEvalMixin property) all_de_metrics (CellEvalMixin property)

all_metrics (CellEvalMixin property) alpha_kl_loss (DeSCOPETrainingArguments attribute) alpha_mse_loss (DeSCOPETrainingArguments attribute)

B

BaseDataset (class in descope.dataset)

BaseInference (class in descope.inference) build_de() (in module descope.utils)

C

CellEvalMixin (class in descope.inference) check_adata_format_consistent_with_epiagent() (in module descope.utils) check_whether_skip_de_metrics() (CellEvalMixin method)

collate_fn() (HFBaseDataset static method) compute_metrics() (CellEvalMixin method) ctrl_name (DeSCOPEDataArguments attribute)

D

DatasetForATAC (class in descope.dataset) DatasetForRNA (class in descope.dataset) descope.arguments module descope.dataset module descope.inference module descope.logging module descope.tokenizer module

descope.trainer module descope.utils module DeSCOPEDataArguments (class in descope.arguments) DeSCOPEModelArguments (class in descope.arguments) DeSCOPETrainer (class in descope.trainer) DeSCOPETrainingArguments (class in descope.arguments) direction_match_on_topk_de() (in module descope.utils) DuplicatedFeatureHandling (class in descope.utils)

E

edistance() (in module descope.utils)

evaluate() (DeSCOPETrainer method) extra_metrics (CellEvalMixin property)

G

gene_embs_file (DeSCOPEDataArguments attribute) get_ctrl_cell_indices() (BaseDataset method)

get_ctrl_cell_indices_for_each_celltype() (HFBaseDataset method) get_logger() (in module descope.logging)

H

HFBaseDataset (class in descope.dataset) HFDatasetForATAC (class in descope.dataset) HFDatasetForRNA (class in descope.dataset)

hidden_act (DeSCOPEModelArguments attribute) hidden_dropout (DeSCOPEModelArguments attribute) hidden_size (DeSCOPEModelArguments attribute)

I

inference() (BaseInference method) InferenceForATAC (class in descope.inference)

InferenceForRNA (class in descope.inference) intersect_adatas_for_celltype_transfer() (in module descope.utils)

K

keep_in_memory (DeSCOPEDataArguments attribute)

L

load_gene_embs() (in module descope.utils) load_gene_names_engine() (in module descope.utils)

load_model() (BaseInference method) (InferenceForATAC method) (InferenceForRNA method)

M

MAIN_INPUT_NAME (BaseDataset attribute) (DatasetForATAC attribute) (DatasetForRNA attribute) (HFBaseDataset attribute) (HFDatasetForATAC attribute) (HFDatasetForRNA attribute) max_pooling (DuplicatedFeatureHandling attribute) mean_pooling (DuplicatedFeatureHandling attribute)

module descope.arguments descope.dataset descope.inference descope.logging descope.tokenizer descope.trainer descope.utils

P

pearson() (in module descope.utils) pearson_delta_on_topk_de() (in module descope.utils) pert_gene_encoder_layers (DeSCOPEModelArguments attribute) preprocess_adata() (BaseDataset method) (BaseInference method) (DatasetForATAC method) (DatasetForRNA method) (InferenceForATAC method) (InferenceForRNA method)

preprocess_atac_perturbation_adata_consistent_with_epiagent() (in module descope.utils) preprocess_rna_perturbation_adata() (in module descope.utils) pretrained_model_name_or_path (DeSCOPETrainingArguments attribute)

R

RANDOM_MAPPING_CONTROL_TO_CONTROL (BaseDataset attribute) (DatasetForATAC attribute) (DatasetForRNA attribute) (HFBaseDataset attribute) (HFDatasetForATAC attribute) (HFDatasetForRNA attribute)

S

save() (UniformFeatureForAnnData method) select_topk_ccres() (in module descope.utils) set_verbosity_critical() (in module descope.logging) set_verbosity_debug() (in module descope.logging)

set_verbosity_error() (in module descope.logging) set_verbosity_info() (in module descope.logging) set_verbosity_warning() (in module descope.logging) setup_root_logger() (in module descope.logging)

T

tokenize() (TokenizerForATAC method) (TokenizerForRNA method) tokenize_adata_to_hf_dataset() (in module descope.tokenizer) tokenize_adata_to_hf_dataset_for_atac() (in module descope.tokenizer)

tokenize_adata_to_hf_dataset_for_rna() (in module descope.tokenizer) tokenized_datasets_dir (DeSCOPEDataArguments attribute) TokenizerForATAC (class in descope.tokenizer) TokenizerForRNA (class in descope.tokenizer) train() (DeSCOPETrainer method)

U

UniformFeatureForAnnData (class in descope.utils)

V

variational_decoder_layers (DeSCOPEModelArguments attribute)

variational_encoder_layers (DeSCOPEModelArguments attribute)

W

write_h5ad() (BaseInference static method)