Index

A

adata_pred_prob() (in module besca.tl.auto_annot) adata_predict() (in module besca.tl.auto_annot) add_anno() (in module besca.tl.sig) add_cell_labeling() (in module besca.Import), [1]

additional_labeling() (in module besca.st), [1] analysis_metadata() (in module besca.export), [1] annotate_cells_clustering() (in module besca.tl), [1] annotate_new_cellnames() (in module besca.tl.rc), [1] assert_adata() (in module besca.Import), [1]

B

batch_correct() (in module besca.tl.bcor), [1] besca.examples.example_function module besca.export module besca.Import module besca.pl module besca.pp module

besca.st module besca.tl module besca.tl.bcor module besca.tl.dge module besca.tl.rc module box_per_ind() (in module besca.pl), [1]

C

celllabel_quant_boxplot() (in module besca.pl), [1] celllabel_quant_stackedbar() (in module besca.pl), [1] celltype_labeling() (in module besca.st), [1] clustering() (in module besca.export), [1] combined_signature_score() (in module besca.tl.sig) compute_signed_score() (in module besca.tl.sig) concate_adata() (in module besca)

convert_ensembl_to_symbol() (in module besca) convert_siggenes() (in module besca.tl.sig) convert_symbol_to_ensembl() (in module besca) convert_to_directed() (in module besca.tl.sig) count_occurrence() (in module besca.tl), [1] count_occurrence_subset() (in module besca.tl), [1] count_occurrence_subset_conditions() (in module besca.tl), [1]

D

detected_genes() (in module besca.pl), [1] dot_heatmap() (in module besca.pl), [1]

dot_heatmap_split() (in module besca.pl), [1] dot_heatmap_split_greyscale() (in module besca.pl), [1] dropouts() (in module besca.pl), [1]

E

export_annotconfig() (in module besca.tl.sig) export_celltype() (in module besca.st), [1] export_clustering() (in module besca.st), [1]

export_cp10k() (in module besca.st), [1] export_metadata() (in module besca.st), [1] export_rank() (in module besca.st), [1] export_regressedOut() (in module besca.st), [1]

F

filter() (in module besca.pp), [1] filter_by_set() (in module besca.tl.sig) filter_gene_list() (in module besca.pp), [1] filter_siggenes() (in module besca.tl.sig) filtering_cells_genes_min() (in module besca.st), [1] filtering_mito_genes_max() (in module besca.st), [1]

fit() (in module besca.tl.auto_annot) flex_dotplot() (in module besca.pl), [1] frac_pos() (in module besca.pp), [1] frac_reads() (in module besca.pp), [1] fraction_counts() (in module besca.pp), [1] function_name() (in module besca.examples.example_function)

G

gene_expr_split() (in module besca.pl), [1] gene_expr_split_stacked() (in module besca.pl), [1] generate_gep() (in module besca.export), [1] get_ameans() (in module besca) get_de() (in module besca.tl.dge), [1]

get_gems() (in module besca.tl.sig) get_means() (in module besca) get_raw() (in module besca) get_similar_geneset() (in module besca.tl.sig) getset() (in module besca.tl.sig)

I

insert_gems() (in module besca.tl.sig)

intersect_genes() (in module besca.tl.auto_annot)

K

kp_cells() (in module besca.pl), [1]

kp_counts() (in module besca.pl), [1] kp_genes() (in module besca.pl), [1]

L

labeling_info() (in module besca.export), [1] library_size() (in module besca.pl), [1] librarysize_overview() (in module besca.pl), [1]

linear_svm() (in module besca.tl.auto_annot) logistic_regression() (in module besca.tl.auto_annot) logistic_regression_elastic() (in module besca.tl.auto_annot) logistic_regression_ovr() (in module besca.tl.auto_annot)

M

make_anno() (in module besca.tl.sig) make_gmtx() (in module besca.tl.sig) match_cluster() (in module besca.tl.sig) match_label() (in module besca.tl.sig) max_counts() (in module besca.pl), [1] max_genes() (in module besca.pl), [1] max_mito() (in module besca.pl), [1] mean_expr() (in module besca.pp), [1] merge_data() (in module besca.tl.auto_annot) module besca.examples.example_function besca.export besca.Import besca.pl besca.pp besca.st besca.tl besca.tl.bcor besca.tl.dge besca.tl.rc

N

naive_merge() (in module besca.tl.auto_annot)

nomenclature_network() (in module besca.pl), [1] normalize_geometric() (in module besca.pp), [1]

O

obtain_dblabel() (in module besca.tl.sig)

obtain_new_label() (in module besca.tl.sig)

P

perform_dge() (in module besca.tl.dge), [1] plot_confusion_matrix() (in module besca.tl), [1] plot_interactive_volcano() (in module besca.tl.dge), [1]

postprocess_mnnpy() (in module besca.tl.bcor), [1] predict() (in module besca.tl.auto_annot) predict_proba() (in module besca.tl.auto_annot) pseudobulk() (in module besca.export), [1]

R

random_forest() (in module besca.tl.auto_annot) ranked_genes() (in module besca.export), [1] raw_to_mtx() (in module besca.export), [1] rbf_svm() (in module besca.tl.auto_annot) read_adata() (in module besca.tl.auto_annot) read_annotconfig() (in module besca.tl.sig) read_data() (in module besca.tl.auto_annot) read_GMT_sign() (in module besca.tl.sig)

read_matrix() (in module besca.st), [1] read_mtx() (in module besca.Import), [1] read_raw() (in module besca.tl.auto_annot) recluster() (in module besca.tl.rc), [1] remove_genes() (in module besca.tl.auto_annot) remove_nonshared() (in module besca.tl.auto_annot) report() (in module besca.tl), [1] (in module besca.tl.auto_annot) riverplot_2categories() (in module besca.pl), [1]

S

scanorama_merge() (in module besca.tl.auto_annot) scanvi_predict() (in module besca.tl.auto_annot) score_mw() (in module besca.tl.sig) scTransform() (in module besca.pp), [1]

scvi_merge() (in module besca.tl.auto_annot) sgd_svm() (in module besca.tl.auto_annot) silhouette_computation() (in module besca.tl.sig) stacked_split_violin() (in module besca.pl), [1] subset_adata() (in module besca)

T

top_counts_genes() (in module besca.pp), [1] top_expressed_genes() (in module besca.pp), [1]

top_genes_counts() (in module besca.pl), [1] transcript_capture_efficiency() (in module besca.pl), [1]

U

update_qualitative_palette() (in module besca.pl), [1]

V

valOutlier() (in module besca.pp), [1]

visualise_scvi_merge() (in module besca.tl.auto_annot)

W

write_gmtx_forgems() (in module besca.tl.sig)

write_labeling_to_files() (in module besca.export), [1]

X

X_to_mtx() (in module besca.export), [1]