sctoolbox API reference

• Tools
  • Preprocessing
    • qc_filter
      • calculate_qc_metrics()
      • predict_cell_cycle()
      • estimate_doublets()
      • predict_sex()
      • automatic_thresholds()
      • thresholds_as_table()
      • validate_threshold_dict()
      • get_thresholds_wrapper()
      • get_keys()
      • get_mean_thresholds()
      • apply_qc_thresholds()
      • filter_cells()
      • filter_genes()
    • highly_variable
      • annot_HVG()
      • get_variable_features()
    • dim_reduction
      • compute_PCA()
      • lsi()
      • apply_svd()
      • define_PC()
      • propose_pcs()
      • subset_PCA()
    • norm_correct
      • atac_norm()
      • normalize_adata()
      • tfidf()
      • tfidf_normalization()
      • wrap_corrections()
      • batch_correction()
      • evaluate_batch_effect()
      • wrap_batch_evaluation()
  • Analysis
    • embedding
      • wrap_umap()
      • correlation_matrix()
    • clustering
      • recluster()
      • gini()
      • calc_ragi()
    • marker_genes
      • get_chromosome_genes()
      • label_genes()
      • add_gene_expression()
      • run_rank_genes()
      • pairwise_rank_genes()
      • get_rank_genes_tables()
      • mask_rank_genes()
      • run_deseq2()
      • score_genes()
    • celltype_annotation
      • add_cellxgene_annotation()
      • get_celltype_assignment()
      • run_scsa()
  • Additional
    • calc_overlap_fc
      • pct_fragments_in_promoters()
      • fc_fragments_in_regions()
      • count_fragments_per_cell()
    • multiomics
      • merge_anndata()
    • bam
      • bam_adata_ov()
      • check_barcode_tag()
      • subset_bam()
      • split_bam_clusters()
      • open_bam()
      • get_bam_reads()
      • bam_to_bigwig()
      • create_fragment_file()
    • frip
      • calc_frip_scores()
    • tsse
      • write_TSS_bed()
      • overlap_and_aggregate()
      • calc_per_base_tsse()
      • global_tsse_score()
      • tsse_scoring()
      • add_tsse_score()
    • insertsize
      • add_insertsize()
    • peak_annotation
      • annotate_adata()
      • annotate_narrowPeak()
    • receptor_ligand
      • download_db()
      • calculate_interaction_table()
      • interaction_violin_plot()
      • hairball()
      • progress_violins()
      • interaction_progress()
      • connectionPlot()
      • get_interactions()
    • gene_correlation
      • correlate_conditions()
      • correlate_ref_vs_all()
      • compare_two_conditons()
    • tobias
      • write_TOBIAS_config()
• Plotting
  • qc_filter
    • plot_starsolo_quality()
    • plot_starsolo_UMI()
    • n_cells_barplot()
    • group_correlation()
    • plot_insertsize()
    • quality_violin()
    • get_slider_thresholds()
  • highly_variable
    • violin_HVF_distribution()
    • scatter_HVF_distribution()
  • embedding
    • sc_colormap()
    • grey_colormap()
    • flip_embedding()
    • plot_embedding()
    • search_umap_parameters()
    • search_tsne_parameters()
    • plot_group_embeddings()
    • compare_embeddings()
    • plot_3D_UMAP()
    • umap_marker_overview()
    • anndata_overview()
    • plot_pca_variance()
    • plot_pca_correlation()
  • clustering
    • search_clustering_parameters()
    • marker_gene_clustering()
  • marker_genes
    • rank_genes_plot()
    • grouped_violin()
    • group_expression_boxplot()
    • gene_expression_heatmap()
    • plot_differential_genes()
    • plot_gene_correlation()
  • genometracks
    • GenomeTracks
      • GenomeTracks.add_track()
      • GenomeTracks.add_hlines()
      • GenomeTracks.add_hline()
      • GenomeTracks.add_spacer()
      • GenomeTracks.add_xaxis()
      • GenomeTracks.show_plot()
      • GenomeTracks.show_config()
      • GenomeTracks.plot()
  • velocity
    • pseudotime_heatmap()
  • general
    • clustermap_dotplot()
    • bidirectional_barplot()
    • boxplot()
    • violinplot()
    • plot_venn()
    • pairwise_scatter()
• Utils
  • creators
    • gitlab_download()
    • setup_experiment()
    • add_analysis()
    • build_notebooks_regex()
  • checker
    • check_module()
    • gunzip_file()
    • is_str_numeric()
    • var_index_from()
    • get_index_type()
    • validate_regions()
    • format_adata_var()
    • in_range()
    • is_integer_array()
    • check_columns()
    • check_file_ending()
    • is_regex()
    • check_marker_lists()
    • check_type()
  • bioutils
    • pseudobulk_table()
    • barcode_index()
    • get_organism()
    • gene_id_to_name()
    • convert_id()
    • unify_genes_column()
  • decorator
    • log_anndata()
    • get_parameter_table()
    • debug_func_log()
  • multiprocessing
    • get_pbar()
    • monitor_jobs()
  • jupyter
    • clear()
  • tables
    • rename_categories()
    • fill_na()
    • write_excel()
    • table_zscore()
  • adata
    • get_adata_subsets()
    • add_expr_to_obs()
    • shuffle_cells()
    • get_minimal_adata()
    • load_h5ad()
    • save_h5ad()
    • add_uns_info()
    • get_cell_values()
    • prepare_for_cellxgene()
  • assemblers
    • prepare_atac_anndata()
    • from_single_starsolo()
    • from_quant()
    • from_single_mtx()
    • from_mtx()
    • convertToAdata()
  • general
    • get_user()
    • get_datetime()
    • get_package_versions()
    • get_binary_path()
    • run_cmd()
    • setup_R()
    • split_list()
    • split_list_size()
    • write_list_file()
    • read_list_file()
    • clean_flanking_strings()
    • longest_common_suffix()
    • remove_prefix()
    • remove_suffix()
    • sanitize_string()
    • identify_columns()
    • scale_values()
  • io
    • create_dir()
    • get_temporary_filename()
    • remove_files()
    • rm_tmp()