Index

A

add_analysis() (in module sctoolbox.utils.creators) add_cellxgene_annotation() (in module sctoolbox.tools.celltype_annotation) add_expr_to_obs() (in module sctoolbox.utils.adata) add_gene_expression() (in module sctoolbox.tools.marker_genes) add_hline() (sctoolbox.plotting.genometracks.GenomeTracks method) add_hlines() (sctoolbox.plotting.genometracks.GenomeTracks method) add_insertsize() (in module sctoolbox.tools.insertsize) add_spacer() (sctoolbox.plotting.genometracks.GenomeTracks method) add_track() (sctoolbox.plotting.genometracks.GenomeTracks method) add_tsse_score() (in module sctoolbox.tools.tsse)

add_uns_info() (in module sctoolbox.utils.adata) add_xaxis() (sctoolbox.plotting.genometracks.GenomeTracks method) anndata_overview() (in module sctoolbox.plotting.embedding) annot_HVG() (in module sctoolbox.tools.highly_variable) annotate_adata() (in module sctoolbox.tools.peak_annotation) annotate_narrowPeak() (in module sctoolbox.tools.peak_annotation) apply_qc_thresholds() (in module sctoolbox.tools.qc_filter) apply_svd() (in module sctoolbox.tools.dim_reduction) atac_norm() (in module sctoolbox.tools.norm_correct) automatic_thresholds() (in module sctoolbox.tools.qc_filter)

B

bam_adata_ov() (in module sctoolbox.tools.bam) bam_to_bigwig() (in module sctoolbox.tools.bam) barcode_index() (in module sctoolbox.utils.bioutils)

batch_correction() (in module sctoolbox.tools.norm_correct) bidirectional_barplot() (in module sctoolbox.plotting.general) boxplot() (in module sctoolbox.plotting.general) build_notebooks_regex() (in module sctoolbox.utils.creators)

C

calc_frip_scores() (in module sctoolbox.tools.frip) calc_per_base_tsse() (in module sctoolbox.tools.tsse) calc_ragi() (in module sctoolbox.tools.clustering) calculate_interaction_table() (in module sctoolbox.tools.receptor_ligand) calculate_qc_metrics() (in module sctoolbox.tools.qc_filter) check_barcode_tag() (in module sctoolbox.tools.bam) check_columns() (in module sctoolbox.utils.checker) check_file_ending() (in module sctoolbox.utils.checker) check_marker_lists() (in module sctoolbox.utils.checker) check_module() (in module sctoolbox.utils.checker) check_type() (in module sctoolbox.utils.checker) clean_flanking_strings() (in module sctoolbox.utils.general) clear() (in module sctoolbox.utils.jupyter)

clustermap_dotplot() (in module sctoolbox.plotting.general) compare_embeddings() (in module sctoolbox.plotting.embedding) compare_two_conditons() (in module sctoolbox.tools.gene_correlation) compute_PCA() (in module sctoolbox.tools.dim_reduction) connectionPlot() (in module sctoolbox.tools.receptor_ligand) convert_id() (in module sctoolbox.utils.bioutils) convertToAdata() (in module sctoolbox.utils.assemblers) correlate_conditions() (in module sctoolbox.tools.gene_correlation) correlate_ref_vs_all() (in module sctoolbox.tools.gene_correlation) correlation_matrix() (in module sctoolbox.tools.embedding) count_fragments_per_cell() (in module sctoolbox.tools.calc_overlap_fc) create_dir() (in module sctoolbox.utils.io) create_fragment_file() (in module sctoolbox.tools.bam)

D

debug_func_log() (in module sctoolbox.utils.decorator)

define_PC() (in module sctoolbox.tools.dim_reduction) download_db() (in module sctoolbox.tools.receptor_ligand)

E

estimate_doublets() (in module sctoolbox.tools.qc_filter)

evaluate_batch_effect() (in module sctoolbox.tools.norm_correct)

F

fc_fragments_in_regions() (in module sctoolbox.tools.calc_overlap_fc) fill_na() (in module sctoolbox.utils.tables) filter_cells() (in module sctoolbox.tools.qc_filter) filter_genes() (in module sctoolbox.tools.qc_filter) flip_embedding() (in module sctoolbox.plotting.embedding)

format_adata_var() (in module sctoolbox.utils.checker) from_mtx() (in module sctoolbox.utils.assemblers) from_quant() (in module sctoolbox.utils.assemblers) from_single_mtx() (in module sctoolbox.utils.assemblers) from_single_starsolo() (in module sctoolbox.utils.assemblers)

G

gene_expression_heatmap() (in module sctoolbox.plotting.marker_genes) gene_id_to_name() (in module sctoolbox.utils.bioutils) GenomeTracks (class in sctoolbox.plotting.genometracks) get_adata_subsets() (in module sctoolbox.utils.adata) get_bam_reads() (in module sctoolbox.tools.bam) get_binary_path() (in module sctoolbox.utils.general) get_cell_values() (in module sctoolbox.utils.adata) get_celltype_assignment() (in module sctoolbox.tools.celltype_annotation) get_chromosome_genes() (in module sctoolbox.tools.marker_genes) get_datetime() (in module sctoolbox.utils.general) get_index_type() (in module sctoolbox.utils.checker) get_interactions() (in module sctoolbox.tools.receptor_ligand) get_keys() (in module sctoolbox.tools.qc_filter) get_mean_thresholds() (in module sctoolbox.tools.qc_filter) get_minimal_adata() (in module sctoolbox.utils.adata) get_organism() (in module sctoolbox.utils.bioutils)

get_package_versions() (in module sctoolbox.utils.general) get_parameter_table() (in module sctoolbox.utils.decorator) get_pbar() (in module sctoolbox.utils.multiprocessing) get_rank_genes_tables() (in module sctoolbox.tools.marker_genes) get_slider_thresholds() (in module sctoolbox.plotting.qc_filter) get_temporary_filename() (in module sctoolbox.utils.io) get_thresholds_wrapper() (in module sctoolbox.tools.qc_filter) get_user() (in module sctoolbox.utils.general) get_variable_features() (in module sctoolbox.tools.highly_variable) gini() (in module sctoolbox.tools.clustering) gitlab_download() (in module sctoolbox.utils.creators) global_tsse_score() (in module sctoolbox.tools.tsse) grey_colormap() (in module sctoolbox.plotting.embedding) group_correlation() (in module sctoolbox.plotting.qc_filter) group_expression_boxplot() (in module sctoolbox.plotting.marker_genes) grouped_violin() (in module sctoolbox.plotting.marker_genes) gunzip_file() (in module sctoolbox.utils.checker)

H

hairball() (in module sctoolbox.tools.receptor_ligand)

I

identify_columns() (in module sctoolbox.utils.general) in_range() (in module sctoolbox.utils.checker) interaction_progress() (in module sctoolbox.tools.receptor_ligand)

interaction_violin_plot() (in module sctoolbox.tools.receptor_ligand) is_integer_array() (in module sctoolbox.utils.checker) is_regex() (in module sctoolbox.utils.checker) is_str_numeric() (in module sctoolbox.utils.checker)

L

label_genes() (in module sctoolbox.tools.marker_genes) load_h5ad() (in module sctoolbox.utils.adata)

log_anndata() (in module sctoolbox.utils.decorator) longest_common_suffix() (in module sctoolbox.utils.general) lsi() (in module sctoolbox.tools.dim_reduction)

M

marker_gene_clustering() (in module sctoolbox.plotting.clustering) mask_rank_genes() (in module sctoolbox.tools.marker_genes) merge_anndata() (in module sctoolbox.tools.multiomics) module sctoolbox.plotting.clustering sctoolbox.plotting.embedding sctoolbox.plotting.general sctoolbox.plotting.genometracks sctoolbox.plotting.highly_variable sctoolbox.plotting.marker_genes sctoolbox.plotting.qc_filter sctoolbox.plotting.velocity sctoolbox.tools.bam sctoolbox.tools.calc_overlap_fc sctoolbox.tools.celltype_annotation sctoolbox.tools.clustering sctoolbox.tools.dim_reduction sctoolbox.tools.embedding sctoolbox.tools.frip sctoolbox.tools.gene_correlation sctoolbox.tools.highly_variable sctoolbox.tools.insertsize sctoolbox.tools.marker_genes sctoolbox.tools.multiomics sctoolbox.tools.norm_correct sctoolbox.tools.peak_annotation sctoolbox.tools.qc_filter sctoolbox.tools.receptor_ligand sctoolbox.tools.tobias sctoolbox.tools.tsse sctoolbox.utils.adata sctoolbox.utils.assemblers sctoolbox.utils.bioutils sctoolbox.utils.checker sctoolbox.utils.creators sctoolbox.utils.decorator sctoolbox.utils.general sctoolbox.utils.io sctoolbox.utils.jupyter sctoolbox.utils.multiprocessing sctoolbox.utils.tables

monitor_jobs() (in module sctoolbox.utils.multiprocessing)

N

n_cells_barplot() (in module sctoolbox.plotting.qc_filter)

normalize_adata() (in module sctoolbox.tools.norm_correct)

O

open_bam() (in module sctoolbox.tools.bam)

overlap_and_aggregate() (in module sctoolbox.tools.tsse)

P

pairwise_rank_genes() (in module sctoolbox.tools.marker_genes) pairwise_scatter() (in module sctoolbox.plotting.general) pct_fragments_in_promoters() (in module sctoolbox.tools.calc_overlap_fc) plot() (sctoolbox.plotting.genometracks.GenomeTracks method) plot_3D_UMAP() (in module sctoolbox.plotting.embedding) plot_differential_genes() (in module sctoolbox.plotting.marker_genes) plot_embedding() (in module sctoolbox.plotting.embedding) plot_gene_correlation() (in module sctoolbox.plotting.marker_genes) plot_group_embeddings() (in module sctoolbox.plotting.embedding) plot_insertsize() (in module sctoolbox.plotting.qc_filter) plot_pca_correlation() (in module sctoolbox.plotting.embedding)

plot_pca_variance() (in module sctoolbox.plotting.embedding) plot_starsolo_quality() (in module sctoolbox.plotting.qc_filter) plot_starsolo_UMI() (in module sctoolbox.plotting.qc_filter) plot_venn() (in module sctoolbox.plotting.general) predict_cell_cycle() (in module sctoolbox.tools.qc_filter) predict_sex() (in module sctoolbox.tools.qc_filter) prepare_atac_anndata() (in module sctoolbox.utils.assemblers) prepare_for_cellxgene() (in module sctoolbox.utils.adata) progress_violins() (in module sctoolbox.tools.receptor_ligand) propose_pcs() (in module sctoolbox.tools.dim_reduction) pseudobulk_table() (in module sctoolbox.utils.bioutils) pseudotime_heatmap() (in module sctoolbox.plotting.velocity)

Q

quality_violin() (in module sctoolbox.plotting.qc_filter)

R

rank_genes_plot() (in module sctoolbox.plotting.marker_genes) read_list_file() (in module sctoolbox.utils.general) recluster() (in module sctoolbox.tools.clustering) remove_files() (in module sctoolbox.utils.io) remove_prefix() (in module sctoolbox.utils.general) remove_suffix() (in module sctoolbox.utils.general)

rename_categories() (in module sctoolbox.utils.tables) rm_tmp() (in module sctoolbox.utils.io) run_cmd() (in module sctoolbox.utils.general) run_deseq2() (in module sctoolbox.tools.marker_genes) run_rank_genes() (in module sctoolbox.tools.marker_genes) run_scsa() (in module sctoolbox.tools.celltype_annotation)

S

sanitize_string() (in module sctoolbox.utils.general) save_h5ad() (in module sctoolbox.utils.adata) sc_colormap() (in module sctoolbox.plotting.embedding) scale_values() (in module sctoolbox.utils.general) scatter_HVF_distribution() (in module sctoolbox.plotting.highly_variable) score_genes() (in module sctoolbox.tools.marker_genes) sctoolbox.plotting.clustering module sctoolbox.plotting.embedding module sctoolbox.plotting.general module sctoolbox.plotting.genometracks module sctoolbox.plotting.highly_variable module sctoolbox.plotting.marker_genes module sctoolbox.plotting.qc_filter module sctoolbox.plotting.velocity module sctoolbox.tools.bam module sctoolbox.tools.calc_overlap_fc module sctoolbox.tools.celltype_annotation module sctoolbox.tools.clustering module sctoolbox.tools.dim_reduction module sctoolbox.tools.embedding module sctoolbox.tools.frip module sctoolbox.tools.gene_correlation module sctoolbox.tools.highly_variable module sctoolbox.tools.insertsize module sctoolbox.tools.marker_genes module sctoolbox.tools.multiomics module

sctoolbox.tools.norm_correct module sctoolbox.tools.peak_annotation module sctoolbox.tools.qc_filter module sctoolbox.tools.receptor_ligand module sctoolbox.tools.tobias module sctoolbox.tools.tsse module sctoolbox.utils.adata module sctoolbox.utils.assemblers module sctoolbox.utils.bioutils module sctoolbox.utils.checker module sctoolbox.utils.creators module sctoolbox.utils.decorator module sctoolbox.utils.general module sctoolbox.utils.io module sctoolbox.utils.jupyter module sctoolbox.utils.multiprocessing module sctoolbox.utils.tables module search_clustering_parameters() (in module sctoolbox.plotting.clustering) search_tsne_parameters() (in module sctoolbox.plotting.embedding) search_umap_parameters() (in module sctoolbox.plotting.embedding) setup_experiment() (in module sctoolbox.utils.creators) setup_R() (in module sctoolbox.utils.general) show_config() (sctoolbox.plotting.genometracks.GenomeTracks method) show_plot() (sctoolbox.plotting.genometracks.GenomeTracks method) shuffle_cells() (in module sctoolbox.utils.adata) split_bam_clusters() (in module sctoolbox.tools.bam) split_list() (in module sctoolbox.utils.general) split_list_size() (in module sctoolbox.utils.general) subset_bam() (in module sctoolbox.tools.bam) subset_PCA() (in module sctoolbox.tools.dim_reduction)

T

table_zscore() (in module sctoolbox.utils.tables) tfidf() (in module sctoolbox.tools.norm_correct)

tfidf_normalization() (in module sctoolbox.tools.norm_correct) thresholds_as_table() (in module sctoolbox.tools.qc_filter) tsse_scoring() (in module sctoolbox.tools.tsse)

U

umap_marker_overview() (in module sctoolbox.plotting.embedding)

unify_genes_column() (in module sctoolbox.utils.bioutils)

V

validate_regions() (in module sctoolbox.utils.checker) validate_threshold_dict() (in module sctoolbox.tools.qc_filter)

var_index_from() (in module sctoolbox.utils.checker) violin_HVF_distribution() (in module sctoolbox.plotting.highly_variable) violinplot() (in module sctoolbox.plotting.general)

W

wrap_batch_evaluation() (in module sctoolbox.tools.norm_correct) wrap_corrections() (in module sctoolbox.tools.norm_correct) wrap_umap() (in module sctoolbox.tools.embedding)

write_excel() (in module sctoolbox.utils.tables) write_list_file() (in module sctoolbox.utils.general) write_TOBIAS_config() (in module sctoolbox.tools.tobias) write_TSS_bed() (in module sctoolbox.tools.tsse)