Index

_

__init__() (UNAGI.train.runner.UNAGI_runner method), [1] (UNAGI.train.trainer.UNAGI_trainer method), [1] (UNAGI.UNAGI method) (UNAGI.UNAGI_analyst.analyst method)

A

analyst (class in UNAGI.UNAGI_analyst)

B

buildEdges() (in module UNAGI.dynamic_graphs.buildGraph)

C

calculate_neighbor_graph() (UNAGI.UNAGI_tool.UNAGI method)

calculateKL() (in module UNAGI.dynamic_graphs.distDistance) cell_type_composition() (in module UNAGI.plotting.plot_cell_type_composition)

G

get_dataset_hcmarkers() (in module UNAGI.marker_discovery.hierachical_static_markers) get_top_compounds() (in module UNAGI.perturbations.compounds)

get_top_pathways() (in module UNAGI.perturbations.pathways) getSimilarity() (in module UNAGI.dynamic_graphs.distDistance) getTopMarkersFromIDREM() (in module UNAGI.marker_discovery.dynamic_markers)

H

hierarchical_static_markers_heatmap() (in module UNAGI.plotting.plot_hierarchical_markers_heatmap)

M

main_analysis() (UNAGI.perturbations.analysis_perturbation.perturbationAnalysis method) module UNAGI.dynamic_graphs.buildGraph UNAGI.dynamic_graphs.distDistance UNAGI.dynamic_regulatory_networks, [1], [2], [3] UNAGI.model, [1] UNAGI.model.models, [1] UNAGI.plotting, [1] UNAGI.plotting.plot_cell_type_composition UNAGI.train, [1] UNAGI.train.customized_elbo, [1] UNAGI.UNAGI_tool.UNAGI, [1]

N

nodesDistance() (in module UNAGI.dynamic_graphs.buildGraph)

normalizeDistance() (in module UNAGI.dynamic_graphs.distDistance)

O

online_analysis() (UNAGI.perturbations.analysis_perturbation.perturbationAnalysis method)

P

plot_hc_dendrogram() (in module UNAGI.plotting.plot_stage_dendrogram)

plot_stages_latent_representation() (in module UNAGI.plotting.plot_cell_embeddings) plot_with_colormap() (in module UNAGI.plotting.plot_cell_embeddings)

R

register_CPO_parameters() (UNAGI.UNAGI_tool.UNAGI method) register_iDREM_parameters() (UNAGI.UNAGI_tool.UNAGI method) register_species() (UNAGI.UNAGI_tool.UNAGI method) reupdateAttributes() (in module UNAGI.dynamic_graphs.buildGraph) run() (UNAGI.perturbations.speedup_perturbation.perturbation method)

run_online() (UNAGI.perturbations.speedup_perturbation.perturbation method) run_UNAGI() (UNAGI.UNAGI_tool.UNAGI method) runGetProgressionMarker() (in module UNAGI.marker_discovery.dynamic_markers) runGetProgressionMarker_one_dist() (in module UNAGI.marker_discovery.dynamic_markers) runGetProgressionMarkercsv() (in module UNAGI.marker_discovery.dynamic_markers) runIdrem() (in module UNAGI.dynamic_regulatory_networks.processIDREM)

S

scoreAgainstBackground() (in module UNAGI.marker_discovery.dynamic_markers) setup_data() (UNAGI.UNAGI_tool.UNAGI method) setup_training() (UNAGI.UNAGI_tool.UNAGI method)

start_analyse() (UNAGI.UNAGI_analyst.analyst method) startAutoPerturbation() (UNAGI.perturbations.speedup_perturbation.perturbation method) startAutoPerturbation_online() (UNAGI.perturbations.speedup_perturbation.perturbation method)

U

UNAGI (class in UNAGI) UNAGI.dynamic_graphs.buildGraph module UNAGI.dynamic_graphs.distDistance module UNAGI.dynamic_regulatory_networks module, [1], [2], [3] UNAGI.model module, [1] UNAGI.model.models module, [1] UNAGI.plotting module, [1]

UNAGI.plotting.plot_cell_type_composition module UNAGI.train module, [1] UNAGI.train.customized_elbo module, [1] UNAGI.UNAGI_tool.UNAGI module, [1] UNAGI_runner (class in UNAGI.train.runner), [1] UNAGI_trainer (class in UNAGI.train.trainer), [1] updataGeneTablesWithDecay() (in module UNAGI.dynamic_regulatory_networks.processTFs) updateEdges() (in module UNAGI.dynamic_graphs.buildGraph)