Index

C

cluster_differential_expression_heatmap() (in module panopticon.visualization) cluster_enrichment_heatmap() (in module panopticon.visualization) cohensd() (in module panopticon.utilities) combine_misshaped_looms() (in module panopticon.utilities) conditional_simpson() (in module panopticon.analysis) convert_10x_h5() (in module panopticon.utilities) convert_h5ad() (in module panopticon.utilities)

convert_to_sparse() (in module panopticon.wme) create_excel_spreadsheet_from_differential_expression_dict() (in module panopticon.utilities) create_gsea_txt_and_cls() (in module panopticon.utilities) create_single_cell_portal_compatible_files() (in module panopticon.utilities) create_split_exon_gtf() (in module panopticon.utilities) create_subsetted_loom() (in module panopticon.legacy) create_subsetted_loom_with_genemask() (in module panopticon.legacy)

D

data_to_grid_kde() (in module panopticon.visualization)

deintify() (in module panopticon.utilities)

G

gene_position_augmentation_main() (in module panopticon.commands.bookem) gene_signature_wizard_main() (in module panopticon.commands.bookem) generate_antibody_prediction() (in module panopticon.preprocessing) generate_ca_frequency() (in module panopticon.utilities) generate_cell_and_gene_quality_metrics() (in module panopticon.preprocessing) generate_clustering() (in module panopticon.analysis) generate_count_normalization() (in module panopticon.preprocessing) generate_diffusion_coordinates() (in module panopticon.analysis) generate_embedding() (in module panopticon.analysis) generate_gene_variances() (in module panopticon.preprocessing) generate_guide_rna_prediction() (in module panopticon.preprocessing) generate_incremental_pca() (in module panopticon.analysis) generate_malignancy_score() (in module panopticon.analysis) generate_masked_module_score() (in module panopticon.analysis) generate_nmf_and_loadings() (in module panopticon.analysis) generate_pca_loadings() (in module panopticon.analysis) generate_standardized_layer() (in module panopticon.preprocessing) get_alpha_concave_hull_polygon() (in module panopticon.utilities) get_cellphonedb_compatible_counts_and_meta() (in module panopticon.utilities) get_clumpiness() (in module panopticon.utilities) get_cluster_differential_expression() (in module panopticon.analysis) get_cluster_differential_expression_heatmap_df() (in module panopticon.utilities) get_cluster_embedding() (in module panopticon.analysis) get_cluster_enrichment_dataframes() (in module panopticon.analysis) get_cluster_markers() (in module panopticon.analysis)

get_cluster_specific_greater_than_cutoff_mask() (in module panopticon.preprocessing) get_clustering_based_outlier_prediction() (in module panopticon.preprocessing) get_complement_contigency_tables() (in module panopticon.utilities) get_cosine_self_similarity() (in module panopticon.analysis) get_cross_column_attribute_heatmap() (in module panopticon.utilities) get_dictionary_of_cluster_means() (in module panopticon.analysis) get_differential_expression_custom() (in module panopticon.analysis) get_differential_expression_dict() (in module panopticon.analysis) get_differential_expression_over_continuum() (in module panopticon.analysis) get_dsb_normalization() (in module panopticon.utilities) get_enrichment_score() (in module panopticon.analysis) get_gsea_with_selenium() (in module panopticon.legacy) get_igraph_from_adjacency() (in module panopticon.utilities) get_list_of_gene_windows() (in module panopticon.wme) get_metafield_breakdown() (in module panopticon.analysis) get_module_score_loom() (in module panopticon.legacy) get_module_score_matrix() (in module panopticon.analysis) get_outlier_removal_mask() (in module panopticon.utilities) get_patient_averaged_table() (in module panopticon.analysis) get_pca_loadings_matrix() (in module panopticon.analysis) get_ranks() (in module panopticon.wme) get_subclustering() (in module panopticon.analysis) get_umap_from_matrix() (in module panopticon.utilities) get_UMI_curve_from_10x_h5() (in module panopticon.utilities) get_valid_gene_info() (in module panopticon.utilities) get_windowed_mean_expression() (in module panopticon.wme)

H

hutcheson_t() (in module panopticon.analysis)

I

import_check() (in module panopticon.utilities)

incorporate_10x_vdj() (in module panopticon.utilities) intify() (in module panopticon.utilities)

K

kt_cluster() (in module panopticon.clustering)

L

leiden_with_silhouette_score() (in module panopticon.clustering)

M

module panopticon.analysis panopticon.clustering panopticon.commands.bookem panopticon.commands.multireference_dna_correspondence panopticon.commands.windowed_mean_expression_clustering panopticon.dna panopticon.legacy panopticon.preprocessing panopticon.utilities panopticon.visualization panopticon.wme

multireference_dna_correspondence() (in module panopticon.dna) multireference_dna_correspondence_main() (in module panopticon.commands.multireference_dna_correspondence)

P

panopticon.analysis module panopticon.clustering module panopticon.commands.bookem module panopticon.commands.multireference_dna_correspondence module panopticon.commands.windowed_mean_expression_clustering module panopticon.dna module panopticon.legacy module

panopticon.preprocessing module panopticon.utilities module panopticon.visualization module panopticon.wme module phi_coefficient() (in module panopticon.utilities) plot_cluster_umap() (in module panopticon.visualization) plot_density() (in module panopticon.visualization) plot_differential_density() (in module panopticon.visualization) plot_subclusters() (in module panopticon.visualization)

R

recover_meta() (in module panopticon.utilities)

repertoire_plot() (in module panopticon.visualization) robust_mean_windowed_expressions() (in module panopticon.wme)

S

scrna2tracer_mapping() (in module panopticon.analysis) segmentation_to_copy_ratio_dict() (in module panopticon.dna) seurat_to_loom() (in module panopticon.utilities)

silhouette_optimized_leiden() (in module panopticon.clustering) simpson() (in module panopticon.analysis) swarmviolin() (in module panopticon.visualization)

T

tcr_levenshtein_distance() (in module panopticon.utilities)

V

volcano() (in module panopticon.visualization)

W

we_can_pickle_it() (in module panopticon.utilities)

we_can_unpickle_it() (in module panopticon.utilities) windowed_mean_expression_clustering_main() (in module panopticon.commands.windowed_mean_expression_clustering)