Index

A

accept_shuffle() (sccross.models.data.ArrayDataset method) (sccross.models.data.Dataset method) (sccross.models.sccross.AnnDataset method) adopt_pretrained_model() (sccross.models.sccross.SCCROSSModel method) aggregate_obs() (in module sccross.data) all_counts() (in module sccross.utils) AnnDataset (class in sccross.models.sccross) AnnDataset_gs (class in sccross.models.sccross)

ArrayDataset (class in sccross.models.data) attach() (sccross.models.utils.EarlyStopping method) (sccross.models.utils.LRScheduler method) (sccross.models.utils.Tensorboard method) (sccross.models.utils.TrainingPlugin method) autodevice() (in module sccross.models.utils) avg_silhouette_width() (in module sccross.metrics) avg_silhouette_width_batch() (in module sccross.metrics)

C

Classifier (class in sccross.models.layers) clean() (sccross.models.data.Dataset method) col_pcc() (in module sccross.utils) col_spr() (in module sccross.utils) col_var() (in module sccross.utils) compile() (sccross.models.sccross.SCCROSSModel method) (sccross.models.utils.Model method) compute_l() (sccross.models.layers.DataEncoder method) (sccross.models.layers.NBDataEncoder method) (sccross.models.layers.VanillaDataEncoder method)

compute_losses() (sccross.models.sccross.SCCROSSTrainer method) compute_losses_first() (sccross.models.sccross.SCCROSSTrainer method) ConfigManager (class in sccross.utils) configure_dataset() (in module sccross.models.sccross) ConstrainedDataFrame (class in sccross.utils) cov_mat() (in module sccross.utils) CROSS (class in sccross.models.sccross)

D

DataDecoder (class in sccross.models.layers) DataEncoder (class in sccross.models.layers) DataLoader (class in sccross.models.data) Dataset (class in sccross.models.data)

DelayedKeyboardInterrupt (class in sccross.utils) densify() (in module sccross.utils) Discriminator (class in sccross.models.layers) Discriminator_gen (class in sccross.models.layers)

E

EarlyStopping (class in sccross.models.utils)

encode_data() (sccross.models.sccross.SCCROSSModel method) extract_rank_genes_groups() (in module sccross.data)

F

fit() (sccross.models.sccross.SCCROSSModel method) (sccross.models.sccross.SCCROSSTrainer method) (sccross.models.utils.Model method) (sccross.models.utils.Trainer method) fit_SCCROSS() (in module sccross.models) format_data() (sccross.models.sccross.SCCROSSTrainer method) forward() (sccross.models.layers.DataDecoder method) (sccross.models.layers.DataEncoder method) (sccross.models.layers.Discriminator method) (sccross.models.layers.Discriminator_gen method) (sccross.models.layers.NBDataDecoder method) (sccross.models.layers.NBDataEncoder method) (sccross.models.layers.Prior method) (sccross.models.layers.ZDecoder method) (sccross.models.layers.ZEncoder method) (sccross.models.layers.ZILNDataDecoder method) (sccross.models.sccross.CROSS method)

foscttm() (in module sccross.metrics) freeze_cells() (sccross.models.sccross.SCCROSSModel method) freeze_running_stats() (in module sccross.models.utils)

G

gen_tf_gene_table() (in module sccross.models.sccross) geneActivity() (in module sccross.data) generate_augment() (sccross.models.sccross.SCCROSSModel method) generate_cross() (sccross.models.sccross.SCCROSSModel method) generate_multiSim() (sccross.models.sccross.SCCROSSModel method) get_chained_attr() (in module sccross.utils) get_default_numpy_dtype() (in module sccross.models.utils) get_logger() (sccross.utils.LogManager method)

get_losses() (sccross.models.sccross.SCCROSSModel method) (sccross.models.sccross.SCCROSSTrainer method) (sccross.models.utils.Model method) (sccross.models.utils.Trainer method) get_metacells() (in module sccross.data) get_rs() (in module sccross.utils) getGeneSetMatrix() (in module sccross.models.sccross) graph_connectivity() (in module sccross.metrics)

I

in_ipynb() (in module sccross.utils)

L

load() (sccross.models.utils.Model static method) load_model() (in module sccross.models) load_state_dict() (sccross.models.sccross.SCCROSSTrainer method) (sccross.models.utils.Trainer method) log_prob() (sccross.models.utils.MSE method) (sccross.models.utils.RMSE method) (sccross.models.utils.ZILN method) (sccross.models.utils.ZIN method) (sccross.models.utils.ZINB method)

logged() (in module sccross.utils) LogManager (class in sccross.utils) LRScheduler (class in sccross.models.utils) lsi() (in module sccross.data)

M

mean_average_precision() (in module sccross.metrics) metacell_corr() (in module sccross.data) metacell_regr() (in module sccross.data) mnn_prior() (in module sccross.data) Model (class in sccross.models.utils) module sccross sccross.data sccross.metrics sccross.models sccross.models.data sccross.models.layers sccross.models.sccross sccross.models.utils sccross.utils

MSE (class in sccross.models.utils)

N

NBDataDecoder (class in sccross.models.layers) NBDataEncoder (class in sccross.models.layers) neighbor_conservation() (in module sccross.metrics) normalize() (sccross.models.layers.DataEncoder method) (sccross.models.layers.NBDataEncoder method) (sccross.models.layers.VanillaDataEncoder method)

normalize_sparse() (in module sccross.models.sccross) normalized_mutual_info() (in module sccross.metrics)

P

ParallelDataLoader (class in sccross.models.data) pcc_mat() (in module sccross.utils) perturbation_difGenes() (sccross.models.sccross.SCCROSSModel method) prepare_shuffle() (sccross.models.data.Dataset method) Prior (class in sccross.models.layers)

prob_or() (in module sccross.utils) prod() (in module sccross.utils) propose_shuffle() (sccross.models.data.ArrayDataset method) (sccross.models.data.Dataset method) (sccross.models.sccross.AnnDataset method)

R

random_split() (sccross.models.data.ArrayDataset method) (sccross.models.sccross.AnnDataset method) rectify() (sccross.utils.ConstrainedDataFrame class method)

report_metrics() (sccross.models.utils.Trainer method) RMSE (class in sccross.models.utils) run_command() (in module sccross.utils)

S

save() (sccross.models.utils.Model method) sccross module SCCROSS (class in sccross.models.sccross) sccross.data module sccross.metrics module sccross.models module sccross.models.data module sccross.models.layers module sccross.models.sccross module

sccross.models.utils module sccross.utils module SCCROSSModel (class in sccross.models.sccross) SCCROSSTrainer (class in sccross.models.sccross) select_decoder() (in module sccross.models.sccross) select_encoder() (in module sccross.models.sccross) seurat_alignment_score() (in module sccross.metrics) shuffle() (sccross.models.data.Dataset method) shuffle_worker() (sccross.models.data.Dataset method) sigmoid() (in module sccross.utils) SingletonMeta (class in sccross.utils) smart_tqdm() (in module sccross.utils) spr_mat() (in module sccross.utils) state_dict() (sccross.models.sccross.SCCROSSTrainer method) (sccross.models.utils.Trainer method)

T

Tensorboard (class in sccross.models.utils) tfidf() (in module sccross.utils) train_step() (sccross.models.sccross.SCCROSSTrainer method) (sccross.models.utils.Trainer method)

Trainer (class in sccross.models.utils) TrainingPlugin (class in sccross.models.utils)

U

unfreeze_cells() (sccross.models.sccross.SCCROSSModel method)

V

val_step() (sccross.models.sccross.SCCROSSTrainer method) (sccross.models.utils.Trainer method)

VanillaDataEncoder (class in sccross.models.layers) verify() (sccross.utils.ConstrainedDataFrame class method)

Z

ZDecoder (class in sccross.models.layers) ZEncoder (class in sccross.models.layers) ZILN (class in sccross.models.utils)

ZILNDataDecoder (class in sccross.models.layers) ZIN (class in sccross.models.utils) ZINB (class in sccross.models.utils)