Index

A

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)

C

CellTypeAnnotationDataset (class in dance.datasets.singlemodality) CellTypeDeconvoDataset (class in dance.datasets.spatial) ClusteringDataset (class in dance.datasets.singlemodality)

CMAE (class in dance.modules.multi_modality.match_modality) (class in dance.modules.multi_modality.predict_modality) 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.pipeline module Data (class in dance.data) DCCA (class in dance.modules.multi_modality.joint_embedding) 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)

F

filter_by_mask() (dance.data.base.BaseData method) filter_cells() (dance.data.base.BaseData method) 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)

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)

G

get_additional_sweep() (in module dance.pipeline) get_atlas_method() (in module main) get_available_data() (dance.datasets.base.BaseDataset class method) get_data() (dance.data.Data method) get_feature() (dance.data.base.BaseData method) get_map_dict() (dance.datasets.singlemodality.CellTypeAnnotationDataset static method) get_sim() (in module main) 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_step3_yaml() (in module dance.pipeline) 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)

H

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

I

ImputationDataset (class in dance.datasets.singlemodality) init_gmm_params() (dance.modules.multi_modality.joint_embedding.scMVAE 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_raw_data() (dance.datasets.base.BaseDataset method)

M

main module 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.pipeline main

MultiModalityDataset (class in dance.datasets.multimodality)

P

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)

R

resume() (dance.modules.multi_modality.match_modality.CMAE method) (dance.modules.multi_modality.predict_modality.CMAE method)

run_similarity_analysis() (in module main) run_step3() (in module dance.pipeline)

S

save() (dance.modules.multi_modality.match_modality.CMAE method) (dance.modules.multi_modality.predict_modality.CMAE method) save_summary_data() (in module dance.pipeline) 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) scMVAE (class in dance.modules.multi_modality.joint_embedding) 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)

set_config() (dance.data.base.BaseData method) set_config_from_dict() (dance.data.base.BaseData method) set_split_idx() (dance.data.base.BaseData method) SpatialLIBDDataset (class in dance.datasets.spatial)

T

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)