Index

_

__init__() (dance.transforms.AnnDataTransform method) (dance.transforms.graph.SpaGCNGraph method)

A

ACTINN (class in dance.modules.single_modality.cell_type_annotation)

AnnDataTransform (class in dance.transforms) append() (dance.data.base.BaseData method)

B

BabelWrapper (class in dance.modules.multi_modality.predict_modality) BaseData (class in dance.data.base) BaseDataset (class in dance.datasets.base)

BaseTransform (class in dance.transforms.base) BatchFeature (class in dance.transforms) build() (dance.modules.single_modality.imputation.DeepImpute method)

C

cal_loss() (dance.modules.single_modality.cell_type_annotation.ScDeepSort method) Card (class in dance.modules.spatial.cell_type_deconvo) CellFeatureBipartiteGraph (class in dance.transforms.graph) CellFeatureGraph (class in dance.transforms.graph) CellGiottoTopicProfile (class in dance.transforms) CellPCA (class in dance.transforms) CellSVD (class in dance.transforms) CellTopicProfile (class in dance.transforms) CellTypeAnnotationDataset (class in dance.datasets.singlemodality) CellTypeDeconvoDataset (class in dance.datasets.spatial)

Celltypist (class in dance.modules.single_modality.cell_type_annotation) CellwiseMaskData (class in dance.transforms) cluster_loss() (dance.modules.single_modality.clustering.ScDCC method) (dance.modules.single_modality.clustering.ScDeepCluster method) ClusteringDataset (class in dance.datasets.singlemodality) CMAE (class in dance.modules.multi_modality.match_modality) (class in dance.modules.multi_modality.predict_modality) Compose (class in dance.transforms) compute_loss() (dance.modules.single_modality.cell_type_annotation.ACTINN method) config (dance.data.base.BaseData property)

D

dance.data module dance.datasets.multimodality module dance.datasets.singlemodality module dance.datasets.spatial module dance.modules.multi_modality.joint_embedding module dance.modules.multi_modality.match_modality module dance.modules.multi_modality.predict_modality module dance.modules.single_modality.cell_type_annotation module dance.modules.single_modality.clustering module dance.modules.single_modality.imputation module dance.modules.spatial.cell_type_deconvo module

dance.modules.spatial.spatial_domain module dance.transforms module dance.transforms.graph module Data (class in dance.data) DCCA (class in dance.modules.multi_modality.joint_embedding) DeepImpute (class in dance.modules.single_modality.imputation) download() (dance.datasets.base.BaseDataset method) (dance.datasets.multimodality.MultiModalityDataset method) (dance.datasets.singlemodality.CellTypeAnnotationDataset method) (dance.datasets.singlemodality.ClusteringDataset method) (dance.datasets.singlemodality.ImputationDataset method) (dance.datasets.spatial.CellTypeDeconvoDataset method) (dance.datasets.spatial.SpatialLIBDDataset method) download_all() (dance.datasets.base.BaseDataset method) (dance.datasets.singlemodality.CellTypeAnnotationDataset method) (dance.datasets.spatial.SpatialLIBDDataset method) DSTG (class in dance.modules.spatial.cell_type_deconvo) DSTGraph (class in dance.transforms.graph)

E

encodeBatch() (dance.modules.single_modality.clustering.ScDCC method) (dance.modules.single_modality.clustering.ScDeepCluster method)

evaluate() (dance.modules.single_modality.cell_type_annotation.ScDeepSort method) (dance.modules.single_modality.imputation.GraphSCI method)

F

FeatureFeatureGraph (class in dance.transforms.graph) FilterCellsScanpy (class in dance.transforms) FilterGenesCommon (class in dance.transforms) FilterGenesMarker (class in dance.transforms) FilterGenesMarkerGini (class in dance.transforms) FilterGenesMatch (class in dance.transforms) FilterGenesPercentile (class in dance.transforms) FilterGenesRegression (class in dance.transforms) FilterGenesScanpy (class in dance.transforms) FilterGenesTopK (class in dance.transforms) FilterScanpy (class in dance.transforms) fit() (dance.modules.multi_modality.joint_embedding.DCCA method) (dance.modules.multi_modality.joint_embedding.ScMoGCNWrapper method) (dance.modules.multi_modality.joint_embedding.scMVAE method) (dance.modules.multi_modality.match_modality.CMAE method) (dance.modules.multi_modality.match_modality.MMVAE method) (dance.modules.multi_modality.match_modality.ScMoGCNWrapper method) (dance.modules.multi_modality.predict_modality.BabelWrapper method) (dance.modules.multi_modality.predict_modality.CMAE method) (dance.modules.multi_modality.predict_modality.MMVAE method) (dance.modules.multi_modality.predict_modality.ScMoGCNWrapper method) (dance.modules.single_modality.cell_type_annotation.ACTINN method) (dance.modules.single_modality.cell_type_annotation.Celltypist method) (dance.modules.single_modality.cell_type_annotation.ScDeepSort method) (dance.modules.single_modality.cell_type_annotation.SingleCellNet method) (dance.modules.single_modality.cell_type_annotation.SVM method) (dance.modules.single_modality.clustering.GraphSC method) (dance.modules.single_modality.clustering.ScDCC method) (dance.modules.single_modality.clustering.ScDeepCluster method) (dance.modules.single_modality.clustering.ScDSC method) (dance.modules.single_modality.clustering.ScTAG method) (dance.modules.single_modality.imputation.DeepImpute method) (dance.modules.single_modality.imputation.GraphSCI method) (dance.modules.spatial.cell_type_deconvo.Card method) (dance.modules.spatial.cell_type_deconvo.DSTG method) (dance.modules.spatial.cell_type_deconvo.SpatialDecon method) (dance.modules.spatial.cell_type_deconvo.SPOTlight method) (dance.modules.spatial.spatial_domain.Louvain method) (dance.modules.spatial.spatial_domain.SpaGCN method) (dance.modules.spatial.spatial_domain.Stagate method) (dance.modules.spatial.spatial_domain.StLouvain method)

fit_with_sampling() (dance.modules.multi_modality.predict_modality.ScMoGCNWrapper method) forward() (dance.modules.multi_modality.joint_embedding.DCCA method) (dance.modules.multi_modality.joint_embedding.JAE method) (dance.modules.multi_modality.joint_embedding.scMVAE method) (dance.modules.multi_modality.match_modality.CMAE method) (dance.modules.multi_modality.match_modality.MMVAE method) (dance.modules.multi_modality.predict_modality.CMAE method) (dance.modules.multi_modality.predict_modality.MMVAE method) (dance.modules.single_modality.clustering.ScDCC method) (dance.modules.single_modality.clustering.ScDeepCluster method) (dance.modules.single_modality.clustering.ScTAG method) (dance.modules.spatial.spatial_domain.Stagate method) forwardAE() (dance.modules.single_modality.clustering.ScDeepCluster method)

G

GeneHoldout (class in dance.transforms) GeneStats (class in dance.transforms) get_available_data() (dance.datasets.base.BaseDataset class method) get_data() (dance.data.Data method) get_feature() (dance.data.base.BaseData method) get_loss() (dance.modules.single_modality.imputation.GraphSCI method) get_map_dict() (dance.datasets.singlemodality.CellTypeAnnotationDataset static method) get_split_data() (dance.data.base.BaseData method)

get_split_idx() (dance.data.base.BaseData method) get_split_mask() (dance.data.base.BaseData method) get_test_data() (dance.data.Data method) get_train_data() (dance.data.Data method) get_val_data() (dance.data.Data method) get_x() (dance.data.Data method) get_y() (dance.data.Data method) GraphSC (class in dance.modules.single_modality.clustering) GraphSCI (class in dance.modules.single_modality.imputation)

H

hexdigest() (dance.datasets.base.BaseDataset method) (dance.transforms.base.BaseTransform method) (dance.transforms.Compose method)

I

ImputationDataset (class in dance.datasets.singlemodality) init_gmm_params() (dance.modules.multi_modality.joint_embedding.scMVAE method) init_model() (dance.modules.single_modality.clustering.ScTAG method) is_complete() (dance.datasets.base.BaseDataset method) (dance.datasets.multimodality.MultiModalityDataset method) (dance.datasets.singlemodality.CellTypeAnnotationDataset method) (dance.datasets.singlemodality.ClusteringDataset method) (dance.datasets.singlemodality.ImputationDataset method) (dance.datasets.spatial.CellTypeDeconvoDataset method) (dance.datasets.spatial.SpatialLIBDDataset method)

is_complete_all() (dance.datasets.base.BaseDataset method) (dance.datasets.singlemodality.CellTypeAnnotationDataset method) (dance.datasets.spatial.SpatialLIBDDataset method)

J

JAE (class in dance.modules.multi_modality.joint_embedding)

JointEmbeddingNIPSDataset (class in dance.datasets.multimodality)

L

load() (dance.modules.multi_modality.joint_embedding.ScMoGCNWrapper method) (dance.modules.multi_modality.match_modality.ScMoGCNWrapper method) load_data() (dance.datasets.base.BaseDataset method) load_model() (dance.modules.single_modality.cell_type_annotation.ScDeepSort method) (dance.modules.single_modality.clustering.ScDeepCluster method) (dance.modules.single_modality.imputation.DeepImpute method) (dance.modules.single_modality.imputation.GraphSCI method)

load_raw_data() (dance.datasets.base.BaseDataset method) Louvain (class in dance.modules.spatial.spatial_domain)

M

MaskData (class in dance.transforms) MMVAE (class in dance.modules.multi_modality.match_modality) (class in dance.modules.multi_modality.predict_modality) ModalityMatchingDataset (class in dance.datasets.multimodality) ModalityPredictionDataset (class in dance.datasets.multimodality) module dance.data dance.datasets.multimodality dance.datasets.singlemodality dance.datasets.spatial dance.modules.multi_modality.joint_embedding dance.modules.multi_modality.match_modality dance.modules.multi_modality.predict_modality dance.modules.single_modality.cell_type_annotation dance.modules.single_modality.clustering dance.modules.single_modality.imputation dance.modules.spatial.cell_type_deconvo dance.modules.spatial.spatial_domain dance.transforms dance.transforms.graph

MorphologyFeatureCNN (class in dance.transforms) MultiModalityDataset (class in dance.datasets.multimodality)

N

NeighborGraph (class in dance.transforms.graph)

P

pairwise_loss() (dance.modules.single_modality.clustering.ScDCC method) PCACellFeatureGraph (class in dance.transforms.graph) predict() (dance.modules.multi_modality.joint_embedding.DCCA method) (dance.modules.multi_modality.joint_embedding.ScMoGCNWrapper method) (dance.modules.multi_modality.joint_embedding.scMVAE method) (dance.modules.multi_modality.match_modality.CMAE method) (dance.modules.multi_modality.match_modality.MMVAE method) (dance.modules.multi_modality.match_modality.ScMoGCNWrapper method) (dance.modules.multi_modality.predict_modality.BabelWrapper method) (dance.modules.multi_modality.predict_modality.CMAE method) (dance.modules.multi_modality.predict_modality.MMVAE method) (dance.modules.multi_modality.predict_modality.ScMoGCNWrapper method) (dance.modules.single_modality.cell_type_annotation.ACTINN method) (dance.modules.single_modality.cell_type_annotation.Celltypist method) (dance.modules.single_modality.cell_type_annotation.ScDeepSort method) (dance.modules.single_modality.cell_type_annotation.SingleCellNet method) (dance.modules.single_modality.cell_type_annotation.SVM method) (dance.modules.single_modality.clustering.GraphSC method) (dance.modules.single_modality.clustering.ScDCC method) (dance.modules.single_modality.clustering.ScDeepCluster method) (dance.modules.single_modality.clustering.ScDSC method) (dance.modules.single_modality.clustering.ScTAG method) (dance.modules.single_modality.imputation.DeepImpute method) (dance.modules.single_modality.imputation.GraphSCI method) (dance.modules.spatial.cell_type_deconvo.Card method) (dance.modules.spatial.cell_type_deconvo.DSTG method) (dance.modules.spatial.cell_type_deconvo.SpatialDecon method) (dance.modules.spatial.cell_type_deconvo.SPOTlight method) (dance.modules.spatial.spatial_domain.Louvain method) (dance.modules.spatial.spatial_domain.SpaGCN method) (dance.modules.spatial.spatial_domain.Stagate method) (dance.modules.spatial.spatial_domain.StLouvain method)

predict_proba() (dance.modules.single_modality.cell_type_annotation.ScDeepSort method) (dance.modules.single_modality.cell_type_annotation.SingleCellNet method) (dance.modules.single_modality.clustering.ScDCC method) (dance.modules.single_modality.clustering.ScDeepCluster method) (dance.modules.single_modality.clustering.ScDSC method) (dance.modules.single_modality.clustering.ScTAG method) (dance.modules.spatial.spatial_domain.SpaGCN method) pretrain() (dance.modules.single_modality.clustering.ScDCC method) (dance.modules.single_modality.clustering.ScDeepCluster method) (dance.modules.single_modality.clustering.ScDSC method) (dance.modules.single_modality.clustering.ScTAG method) PseudoMixture (class in dance.transforms)

R

random_batches() (dance.modules.single_modality.cell_type_annotation.ACTINN method) randomize() (dance.modules.single_modality.cell_type_annotation.SingleCellNet method) regress_out() (dance.transforms.SpatialIDEFeature method)

RemoveSplit (class in dance.transforms) resume() (dance.modules.multi_modality.match_modality.CMAE method) (dance.modules.multi_modality.predict_modality.CMAE method)

S

save() (dance.modules.multi_modality.match_modality.CMAE method) (dance.modules.multi_modality.predict_modality.CMAE method) (dance.modules.single_modality.cell_type_annotation.SVM method) save_model() (dance.modules.single_modality.cell_type_annotation.ScDeepSort method) (dance.modules.single_modality.clustering.ScDeepCluster method) (dance.modules.single_modality.imputation.DeepImpute method) (dance.modules.single_modality.imputation.GraphSCI method) SaveRaw (class in dance.transforms) ScaleFeature (class in dance.transforms) ScDCC (class in dance.modules.single_modality.clustering) ScDeepCluster (class in dance.modules.single_modality.clustering) ScDeepSort (class in dance.modules.single_modality.cell_type_annotation) ScDSC (class in dance.modules.single_modality.clustering) ScMoGCNWrapper (class in dance.modules.multi_modality.joint_embedding) (class in dance.modules.multi_modality.match_modality) (class in dance.modules.multi_modality.predict_modality) ScMoGNNGraph (class in dance.transforms.graph) scMVAE (class in dance.modules.multi_modality.joint_embedding) SCNFeature (class in dance.transforms) score() (dance.modules.multi_modality.joint_embedding.DCCA method) (dance.modules.multi_modality.joint_embedding.ScMoGCNWrapper method) (dance.modules.multi_modality.joint_embedding.scMVAE method) (dance.modules.multi_modality.match_modality.CMAE method) (dance.modules.multi_modality.match_modality.MMVAE method) (dance.modules.multi_modality.match_modality.ScMoGCNWrapper method) (dance.modules.multi_modality.predict_modality.BabelWrapper method) (dance.modules.multi_modality.predict_modality.CMAE method) (dance.modules.multi_modality.predict_modality.MMVAE method) (dance.modules.multi_modality.predict_modality.ScMoGCNWrapper method) (dance.modules.single_modality.imputation.DeepImpute method) (dance.modules.single_modality.imputation.GraphSCI method)

ScTAG (class in dance.modules.single_modality.clustering) ScTransform (class in dance.transforms) search_l() (dance.modules.spatial.spatial_domain.SpaGCN method) search_set_res() (dance.modules.spatial.spatial_domain.SpaGCN method) set_config() (dance.data.base.BaseData method) set_config_from_dict() (dance.data.base.BaseData method) set_l() (dance.modules.spatial.spatial_domain.SpaGCN method) set_split_idx() (dance.data.base.BaseData method) SetConfig (class in dance.transforms) SingleCellNet (class in dance.modules.single_modality.cell_type_annotation) SMEFeature (class in dance.transforms) SMEGraph (class in dance.transforms.graph) soft_assign() (dance.modules.single_modality.clustering.ScDCC method) (dance.modules.single_modality.clustering.ScDeepCluster method) (dance.modules.single_modality.clustering.ScTAG method) SpaGCN (class in dance.modules.spatial.spatial_domain) SpaGCNGraph (class in dance.transforms.graph) SpaGCNGraph2D (class in dance.transforms.graph) SpatialDecon (class in dance.modules.spatial.cell_type_deconvo) SpatialIDEFeature (class in dance.transforms) SpatialLIBDDataset (class in dance.datasets.spatial) SPOTlight (class in dance.modules.spatial.cell_type_deconvo) stabilize() (dance.transforms.SpatialIDEFeature method) Stagate (class in dance.modules.spatial.spatial_domain) StagateGraph (class in dance.transforms.graph) StLouvain (class in dance.modules.spatial.spatial_domain) SVM (class in dance.modules.single_modality.cell_type_annotation)

T

target_distribution() (dance.modules.single_modality.clustering.ScDCC method) (dance.modules.single_modality.clustering.ScDeepCluster method) (dance.modules.single_modality.clustering.ScDSC method) (dance.modules.single_modality.clustering.ScTAG method)

to() (dance.modules.multi_modality.joint_embedding.ScMoGCNWrapper method) (dance.modules.multi_modality.match_modality.ScMoGCNWrapper method) (dance.modules.multi_modality.predict_modality.BabelWrapper method) train() (dance.modules.single_modality.imputation.GraphSCI method)

W

WeightedFeaturePCA (class in dance.transforms)

wMSE() (dance.modules.single_modality.imputation.DeepImpute method)