Index

A

Analysis (class in Topyfic.analysis)

average_cell_participation() (Topyfic.analysis.Analysis method) average_cell_participation_line_plot() (Topyfic.analysis.Analysis method)

C

calculate_cell_participation() (Topyfic.analysis.Analysis method) calculate_leiden_clustering() (in module Topyfic.utilsMakeModel) cell_participation_distribution() (Topyfic.analysis.Analysis method)

combine_LDA_models() (Topyfic.train.Train method) combine_topModels() (in module Topyfic.utilsMakeModel) compare_topModels() (in module Topyfic.utilsAnalyseModel) convertDatTraits() (Topyfic.analysis.Analysis static method)

E

extract_cells() (Topyfic.analysis.Analysis method)

F

filter_LDA_model() (in module Topyfic.utilsMakeModel)

functional_enrichment_analysis() (in module Topyfic.utilsAnalyseModel) (Topyfic.topic.Topic method)

G

gene_weight_rank_heatmap() (Topyfic.topModel.TopModel method) gene_weight_variance() (Topyfic.topic.Topic method) get_feature_name() (Topyfic.topModel.TopModel method) get_gene_weights() (Topyfic.topModel.TopModel method)

get_ranked_gene_weight() (Topyfic.topModel.TopModel method) get_top_model_attributes() (Topyfic.topModel.TopModel method) GSEA() (in module Topyfic.utilsAnalyseModel) (Topyfic.topic.Topic method)

I

initialize_lda_model() (in module Topyfic.utilsMakeModel)

initialize_rLDA_model() (in module Topyfic.utilsMakeModel)

M

MA_plot() (in module Topyfic.utilsAnalyseModel) (Topyfic.topModel.TopModel method) make_analysis_class() (in module Topyfic.utilsMakeModel) make_LDA_models_attributes() (Topyfic.train.Train method) make_single_LDA_model() (Topyfic.train.Train method) make_topModel() (in module Topyfic.utilsMakeModel) max_topic_cell_participation() (Topyfic.analysis.Analysis method)

modified_zscore() (in module Topyfic.utilsAnalyseModel) module Topyfic.analysis Topyfic.topic Topyfic.topModel Topyfic.train Topyfic.utilsAnalyseModel Topyfic.utilsMakeModel

P

pie_structure_Chart() (Topyfic.analysis.Analysis method)

plot_cluster_contribution() (in module Topyfic.utilsMakeModel) plot_topic_composition() (Topyfic.analysis.Analysis method)

R

read_analysis() (in module Topyfic.utilsMakeModel) read_model_yaml() (in module Topyfic.utilsMakeModel)

read_topModel() (in module Topyfic.utilsMakeModel) read_train() (in module Topyfic.utilsMakeModel) run_LDA_models() (Topyfic.train.Train method)

S

save_analysis() (Topyfic.analysis.Analysis method) save_rLDA_model() (Topyfic.topModel.TopModel method) save_topModel() (Topyfic.topModel.TopModel method)

save_train() (Topyfic.train.Train method) structure_plot() (Topyfic.analysis.Analysis method) subset_data() (in module Topyfic.utilsMakeModel) summarize_GO_Term() (in module Topyfic.utilsAnalyseModel)

T

Topic (class in Topyfic.topic) TopicTraitRelationshipHeatmap() (Topyfic.analysis.Analysis method) TopModel (class in Topyfic.topModel) Topyfic.analysis module Topyfic.topic module Topyfic.topModel module

Topyfic.train module Topyfic.utilsAnalyseModel module Topyfic.utilsMakeModel module Train (class in Topyfic.train) train_model() (in module Topyfic.utilsMakeModel)

U

update_gene_information() (Topyfic.topic.Topic method)

W

write_topic_yaml() (Topyfic.topic.Topic method)