Index

A

adj_to_bias() (in module pytrance.models.DGI.utils.process)

aggregate_transcript_embeddings() (in module pytrance.tools) AvgReadout (class in pytrance.models.DGI.layers.readout)

C

CellData (class in pytrance.data.celldata) cells_in_grid() (in module pytrance.plotting) clq() (in module pytrance.cell_score) clq_pairwise() (in module pytrance.cell_score) clq_significance() (in module pytrance.cell_score)

clq_single_cell() (in module pytrance.cell_score) cluster_gene_embeddings() (in module pytrance.tools) cluster_gene_embeddings_leiden() (in module pytrance.tools) compute_embeddings() (in module pytrance.gnn) compute_figure_size() (in module pytrance.utils)

D

data (pytrance.data.celldata.CellData attribute), [1] dendrogram() (in module pytrance.plotting)

DGI (class in pytrance.models.DGI.models.dgi) disc (pytrance.models.DGI.models.dgi.DGI attribute) Discriminator (class in pytrance.models.DGI.layers.discriminator)

E

embed() (pytrance.models.DGI.models.dgi.DGI method)

embedding_pca() (in module pytrance.plotting) (in module pytrance.tools)

F

f_k (pytrance.models.DGI.layers.discriminator.Discriminator attribute) fc (pytrance.models.DGI.layers.gcn.GCN attribute) (pytrance.models.DGI.models.logreg.LogReg attribute) forward() (pytrance.models.DGI.layers.discriminator.Discriminator method) (pytrance.models.DGI.layers.gcn.GCN method) (pytrance.models.DGI.layers.readout.AvgReadout method) (pytrance.models.DGI.models.dgi.DGI method) (pytrance.models.DGI.models.logreg.LogReg method)

G

GCN (class in pytrance.models.DGI.layers.gcn) get_gene_subclusters() (in module pytrance.utils)

get_neighbors() (in module pytrance.utils) get_tree_linkage() (in module pytrance.utils)

L

layer_type (pytrance.models.DGI.models.dgi.DGI attribute) layers (pytrance.models.DGI.models.dgi.DGI attribute)

load_data() (in module pytrance.models.DGI.utils.process) LogReg (class in pytrance.models.DGI.models.logreg)

M

mask() (in module pytrance.plotting) micro_f1() (in module pytrance.models.DGI.utils.process) module pytrance pytrance.cell_score pytrance.data pytrance.data.celldata pytrance.gnn pytrance.models pytrance.models.DGI pytrance.models.DGI.layers pytrance.models.DGI.layers.discriminator pytrance.models.DGI.layers.gcn pytrance.models.DGI.layers.readout pytrance.models.DGI.models pytrance.models.DGI.models.dgi pytrance.models.DGI.models.logreg pytrance.models.DGI.utils pytrance.models.DGI.utils.process pytrance.plotting pytrance.tools pytrance.utils

N

normalize_adj() (in module pytrance.models.DGI.utils.process)

O

out_features (pytrance.models.DGI.layers.gcn.GCN attribute)

P

pairwise_clq_heatmap() (in module pytrance.plotting) parse_index_file() (in module pytrance.models.DGI.utils.process) parse_skipgram() (in module pytrance.models.DGI.utils.process) preprocess_adj() (in module pytrance.models.DGI.utils.process) preprocess_features() (in module pytrance.models.DGI.utils.process) process_tu() (in module pytrance.models.DGI.utils.process) pytrance module pytrance.cell_score module pytrance.data module pytrance.data.celldata module pytrance.gnn module pytrance.models module pytrance.models.DGI module pytrance.models.DGI.layers module

pytrance.models.DGI.layers.discriminator module pytrance.models.DGI.layers.gcn module pytrance.models.DGI.layers.readout module pytrance.models.DGI.models module pytrance.models.DGI.models.dgi module pytrance.models.DGI.models.logreg module pytrance.models.DGI.utils module pytrance.models.DGI.utils.process module pytrance.plotting module pytrance.tools module pytrance.utils module

R

read (pytrance.models.DGI.models.dgi.DGI attribute)

S

sample_mask() (in module pytrance.models.DGI.utils.process) sigm (pytrance.models.DGI.models.dgi.DGI attribute) sparse_mx_to_torch_sparse_tensor() (in module pytrance.models.DGI.utils.process) (in module pytrance.utils)

sparse_to_tuple() (in module pytrance.models.DGI.utils.process) standardize_data() (in module pytrance.models.DGI.utils.process) subcluster() (in module pytrance.tools)

T

train() (in module pytrance.gnn)

train_epoch() (in module pytrance.gnn) transcripts_histogram() (in module pytrance.plotting)

W

weights_init() (pytrance.models.DGI.layers.discriminator.Discriminator method) (pytrance.models.DGI.layers.gcn.GCN method) (pytrance.models.DGI.models.logreg.LogReg method)