Index

_

__init__() (scdynomics.FT_Encoder method) (scdynomics.FT_Masked_Tuner method) (scdynomics.FT_MLP_Classifier method) (scdynomics.Masked_Pretrainer method) (scdynomics.utils.data.corpus.Multimodal_Corpus method) (scdynomics.utils.data.corpus.Repr_Corpus method) (scdynomics.utils.data.corpus.Tensor_Corpus method) (scdynomics.utils.data.Multimodal_Corpus method) (scdynomics.utils.data.Repr_Corpus method) (scdynomics.utils.data.Tensor_Corpus method) (scdynomics.utils.ref.Maker method)

A

align_genes_to_reference() (in module scdynomics.utils.pp.align)

align_peaks_to_reference() (in module scdynomics.utils.pp.align)

B

bimodal_pretrain() (in module scdynomics)

C

cal_accum_grad_batches() (in module scdynomics.utils.trainer) cal_grad_norm() (scdynomics.FT_MLP_Classifier method) (scdynomics.Masked_Pretrainer method)

configure_optimizers() (scdynomics.FT_MLP_Classifier method) (scdynomics.Masked_Pretrainer method) cpm_promoter() (in module scdynomics.utils.pp.normalize) csv() (in module scdynomics.utils.data.reader)

D

decode() (in module scdynomics.utils.json)

E

encode() (in module scdynomics.utils.json)

explain() (scdynomics.FT_MLP_Classifier method) explaining() (scdynomics.FT_MLP_Classifier method)

F

filter_multimodal_adata() (in module scdynomics.utils.pp.qc) forward() (scdynomics.FT_Encoder method) (scdynomics.FT_MLP_Classifier method) (scdynomics.Masked_Pretrainer method) ft_clf_explain() (in module scdynomics)

ft_clf_predict() (in module scdynomics) FT_Encoder (class in scdynomics) ft_kfold_classification() (in module scdynomics) FT_Masked_Tuner (class in scdynomics) FT_MLP_Classifier (class in scdynomics)

G

get_class_distribution() (scdynomics.utils.data.corpus.Tensor_Corpus method) (scdynomics.utils.data.Tensor_Corpus method) get_confmat() (scdynomics.FT_MLP_Classifier method)

get_init_embedding() (scdynomics.FT_Encoder method) (scdynomics.FT_MLP_Classifier method) get_peak_promoter_map() (in module scdynomics.utils.pp.align)

K

kfold_random_split() (in module scdynomics.utils.data) (in module scdynomics.utils.data.splitter)

L

l1_normalize() (in module scdynomics.utils) (in module scdynomics.utils.pp.normalize)

load_epdnew_tss() (scdynomics.utils.ref.Maker method)

M

make_callbacks() (in module scdynomics.utils.trainer) make_peak_interval_tree() (in module scdynomics.utils.pp.align) Maker (class in scdynomics.utils.ref) Masked_Pretrainer (class in scdynomics) mex() (in module scdynomics.utils.data.reader) module scdynomics.utils scdynomics.utils.data scdynomics.utils.data.corpus scdynomics.utils.data.reader scdynomics.utils.data.splitter scdynomics.utils.json scdynomics.utils.pp scdynomics.utils.pp.align scdynomics.utils.pp.normalize scdynomics.utils.pp.qc scdynomics.utils.ref scdynomics.utils.trainer

mtx() (in module scdynomics.utils.data.reader) Multimodal_Corpus (class in scdynomics.utils.data) (class in scdynomics.utils.data.corpus)

N

normalize_adata() (in module scdynomics.utils.pp.normalize)

O

output_dict() (scdynomics.utils.ref.Maker method)

output_gex_index() (scdynomics.utils.ref.Maker method)

P

parse_peak_id() (in module scdynomics.utils.pp.align) partition() (scdynomics.Masked_Pretrainer method)

pipeline() (in module scdynomics.utils.pp) predict() (scdynomics.FT_MLP_Classifier method)

Q

qc_metrics() (in module scdynomics.utils.pp.qc)

R

random_split() (in module scdynomics.utils.data) (in module scdynomics.utils.data.splitter)

remove_mt_genes() (in module scdynomics.utils.pp.align) Repr_Corpus (class in scdynomics.utils.data) (class in scdynomics.utils.data.corpus)

S

scdynomics.utils module scdynomics.utils.data module scdynomics.utils.data.corpus module scdynomics.utils.data.reader module scdynomics.utils.data.splitter module scdynomics.utils.json module scdynomics.utils.pp module scdynomics.utils.pp.align module scdynomics.utils.pp.normalize module

scdynomics.utils.pp.qc module scdynomics.utils.ref module scdynomics.utils.trainer module scMultiomics_10x_h5() (in module scdynomics.utils.data.reader) scMultiomics_10x_mex() (in module scdynomics.utils.data.reader) scMultiomics_csv_split() (in module scdynomics.utils.data.reader) scMultiomics_mex_split() (in module scdynomics.utils.data.reader) set_accelerator() (in module scdynomics.utils.trainer) stratify() (scdynomics.utils.data.corpus.Multimodal_Corpus method) (scdynomics.utils.data.corpus.Tensor_Corpus method) (scdynomics.utils.data.Multimodal_Corpus method) (scdynomics.utils.data.Tensor_Corpus method) stratify_genes_to_reference() (in module scdynomics.utils.pp.align)

T

Tensor_Corpus (class in scdynomics.utils.data) (class in scdynomics.utils.data.corpus) test_step() (scdynomics.FT_MLP_Classifier method) (scdynomics.Masked_Pretrainer method) to_dev() (scdynomics.Masked_Pretrainer method)

token_tensor (scdynomics.Masked_Pretrainer property) tpm() (in module scdynomics.utils.pp.normalize) training_step() (scdynomics.FT_MLP_Classifier method) (scdynomics.Masked_Pretrainer method) tsv() (in module scdynomics.utils.data.reader)

U

unfreeze_embedder() (scdynomics.FT_Encoder method)

V

validation_step() (scdynomics.FT_MLP_Classifier method) (scdynomics.Masked_Pretrainer method)