Index A | B | C | D | E | F | G | L | R | S | U | V A active_genes_heatmap() (in module scatrans.pl) active_score() (in module scatrans) active_score_rankplot() (in module scatrans.pl) active_score_simple() (in module scatrans) add_gene_features() (in module scatrans) B bias_diagnostic_plot() (in module scatrans.pl) C comet_plot() (in module scatrans.pl) compare_enrichment() (in module scatrans) concat_compare_results() (in module scatrans) D diagnose_design() (in module scatrans) differential_expression() (in module scatrans) differential_expression_simple() (in module scatrans) E enrich_barplot() (in module scatrans.pl) enrich_dotplot() (in module scatrans.pl) enrich_upsetplot() (in module scatrans.pl) enrich_vennplot() (in module scatrans.pl) ensure_raw_counts() (in module scatrans) expand_enrichment_genes() (in module scatrans) extract_gene_lists() (in module scatrans) F figure_export_context() (in module scatrans.pl) filter_active_genes() (in module scatrans) G gamma_shrinkage_plot() (in module scatrans.pl) generate_gene_features_from_gtf() (in module scatrans) gseaplot() (in module scatrans.pl) L list_available_gene_features() (in module scatrans) list_bundled_gene_sets() (in module scatrans) R recommend_workflow() (in module scatrans) restore_raw_counts() (in module scatrans) run_default_pipeline() (in module scatrans) run_enrichment() (in module scatrans) run_go() (in module scatrans) run_gsea() (in module scatrans) run_kegg() (in module scatrans) S save_all_figures() (in module scatrans.pl) save_enrichment_report() (in module scatrans) set_nature_style() (in module scatrans.pl) set_style() (in module scatrans.pl) simplify_enrichment() (in module scatrans) store_raw_counts() (in module scatrans) style_context() (in module scatrans.pl) U unspliced_global() (in module scatrans.qc) V velocity_phase_portraits() (in module scatrans.pl) volcano_3d() (in module scatrans.pl) volcano_plot() (in module scatrans.pl)