Index

_

__init__() (SIDISH.SIDISH method)

A

adata (SIDISH.in_silico_perturbation.InSilicoPerturbation attribute) adjust_expression() (SIDISH.gene_perturbation_utils.GenePerturbationUtils static method) analyze_perturbation_effects() (SIDISH.SIDISH.SIDISH method)

annotateCells() (SIDISH.SIDISH.SIDISH method) (SIDISH.Utils.Utils method) ARCHITECTURE (class in SIDISH.VAE_ARCHITECTURE)

C

create_pytorch_geometric_data() (in module SIDISH.Utils)

create_spatial_graph() (in module SIDISH.Utils)

D

Decoder (class in SIDISH.VAE_ARCHITECTURE)

DEEPCOX (class in SIDISH.DEEP_COX) DEEPCOX_ARCHITECTURE (class in SIDISH.DEEP_COX_ARCHITECTURE)

E

Encoder (class in SIDISH.VAE_ARCHITECTURE)

extractFeature() (in module SIDISH.Utils)

F

forward() (SIDISH.DEEP_COX_ARCHITECTURE.DEEPCOX_ARCHITECTURE method) (SIDISH.VAE_ARCHITECTURE.ARCHITECTURE method) (SIDISH.VAE_ARCHITECTURE.Decoder method) (SIDISH.VAE_ARCHITECTURE.Encoder method) (SIDISH.VAE_ARCHITECTURE.GraphConvLayer method) (SIDISH.VAE_ARCHITECTURE.SpatialEncoder method) (SIDISH.VAE_ARCHITECTURE.SpatialPreEncoder method)

G

GenePerturbationUtils (class in SIDISH.gene_perturbation_utils) genes (SIDISH.in_silico_perturbation.InSilicoPerturbation attribute) get_base_latent_representation() (SIDISH.VAE_ARCHITECTURE.ARCHITECTURE method) get_cogenes() (SIDISH.gene_perturbation_utils.GenePerturbationUtils static method) get_embedding() (SIDISH.SIDISH.SIDISH method) get_latent_representation() (SIDISH.VAE_ARCHITECTURE.ARCHITECTURE method) get_MarkerGenes() (SIDISH.SIDISH.SIDISH method) get_neighbors() (SIDISH.ppi_network_handler.PPINetworkHandler method) get_percentille() (SIDISH.SIDISH.SIDISH method) get_spatial_graph_from_adata() (in module SIDISH.Utils) get_test_ci() (SIDISH.DEEP_COX.DEEPCOX method)

get_test_loss() (SIDISH.DEEP_COX.DEEPCOX method) get_threshold() (SIDISH.Utils.Utils method) get_train_ci() (SIDISH.DEEP_COX.DEEPCOX method) get_train_loss() (SIDISH.DEEP_COX.DEEPCOX method) getBaseEmbedding() (SIDISH.VAE.VAE method) getBaseEncoder() (SIDISH.VAE.VAE method) getEmbedding() (SIDISH.VAE.VAE method) getEmbedding_adata() (SIDISH.SIDISH.SIDISH method) getLoss() (SIDISH.VAE.VAE method) getWeightMatrix() (SIDISH.Utils.Utils method) getWeightVector() (SIDISH.Utils.Utils method) GraphConvLayer (class in SIDISH.VAE_ARCHITECTURE)

I

init_Phase1() (SIDISH.SIDISH.SIDISH method), [1] init_Phase2() (SIDISH.SIDISH.SIDISH method), [1]

initialize() (SIDISH.VAE.VAE method) InSilicoPerturbation (class in SIDISH.in_silico_perturbation)

K

kl_d() (SIDISH.VAE_ARCHITECTURE.ARCHITECTURE method)

knockout_gene() (SIDISH.gene_perturbation_utils.GenePerturbationUtils static method)

L

load_network() (SIDISH.ppi_network_handler.PPINetworkHandler method)

loss_DeepCox() (in module SIDISH.DEEP_COX) loss_function() (SIDISH.VAE_ARCHITECTURE.ARCHITECTURE method)

M

map_event_column() (in module SIDISH.SIDISH) module SIDISH SIDISH.DEEP_COX SIDISH.DEEP_COX_ARCHITECTURE SIDISH.gene_perturbation_utils SIDISH.in_silico_perturbation SIDISH.ppi_network_handler SIDISH.SIDISH, [1] SIDISH.SIDISH.SIDISH, [1], [2], [3], [4] SIDISH.Utils SIDISH.VAE SIDISH.VAE_ARCHITECTURE

P

plot_CellType_UMAP() (SIDISH.SIDISH.SIDISH method) plot_double_Perturbation_Heatmap() (SIDISH.SIDISH.SIDISH method) plot_HighRisk_UMAP() (SIDISH.SIDISH.SIDISH method) plot_KM() (SIDISH.SIDISH.SIDISH method) plot_perturbation_UMAP_default() (SIDISH.SIDISH.SIDISH method) plot_perturbation_UMAP_differential() (SIDISH.SIDISH.SIDISH method) plot_top_perturbed_genes() (SIDISH.SIDISH.SIDISH method)

plot_umap() (in module SIDISH.SIDISH) plot_umap_differential() (in module SIDISH.SIDISH) plotUMAP() (SIDISH.SIDISH.SIDISH method) ppi_handler (SIDISH.in_silico_perturbation.InSilicoPerturbation attribute) PPINetworkHandler (class in SIDISH.ppi_network_handler) preprocess() (in module SIDISH.SIDISH) process_Data() (in module SIDISH.SIDISH) process_gene() (SIDISH.in_silico_perturbation.InSilicoPerturbation method)

R

r_squared() (in module SIDISH.Utils) reconstruction_loss() (SIDISH.VAE_ARCHITECTURE.ARCHITECTURE method) reload() (SIDISH.SIDISH.SIDISH method) reparameterize() (SIDISH.VAE_ARCHITECTURE.ARCHITECTURE method)

run_double_Perturbation() (SIDISH.SIDISH.SIDISH method) run_double_Perturbation_score() (SIDISH.SIDISH.SIDISH method) run_parallel_processing() (SIDISH.in_silico_perturbation.InSilicoPerturbation method) run_Perturbation() (SIDISH.SIDISH.SIDISH method)

S

set_adata() (SIDISH.SIDISH.SIDISH method) setup_ppi_network() (SIDISH.in_silico_perturbation.InSilicoPerturbation method) SIDISH module SIDISH (class in SIDISH) (class in SIDISH.SIDISH) sidish (SIDISH.in_silico_perturbation.InSilicoPerturbation attribute) SIDISH.DEEP_COX module SIDISH.DEEP_COX_ARCHITECTURE module SIDISH.gene_perturbation_utils module SIDISH.in_silico_perturbation module

SIDISH.ppi_network_handler module SIDISH.SIDISH module, [1] SIDISH.SIDISH.SIDISH module, [1], [2], [3], [4] SIDISH.Utils module SIDISH.VAE module SIDISH.VAE_ARCHITECTURE module sigmoid() (in module SIDISH.Utils) SpatialEncoder (class in SIDISH.VAE_ARCHITECTURE) SpatialPreEncoder (class in SIDISH.VAE_ARCHITECTURE)

T

train() (SIDISH.DEEP_COX.DEEPCOX method) (SIDISH.SIDISH.SIDISH method), [1] (SIDISH.VAE.VAE method)

U

Utils (class in SIDISH.Utils)

V

VAE (class in SIDISH.VAE)