API for Yutong441/TBdev
Infer a Trophoblast Developmental Trajectory
| Global functions | |
|---|---|
| Ax3D | Man page Source code |
| CT | Man page |
| DE_gene_pairwise_list | Man page |
| DE_lineage_genes | Man page |
| DimPlot_3D | Man page |
| DimPlot_labels | Man page |
| GOsimp | Man page |
| KeggID | Man page |
| Lab3D | Man page Source code |
| RunDiffusion | Man page |
| RunGPLVM | Man page |
| Seg3D | Man page Source code |
| Stat3D | Man page Source code |
| TF | Man page |
| TF_enrichment_pairwise | Man page |
| add_custom_color | Man page |
| add_level_to_factor | Man page |
| add_min_max | Man page |
| all_pathways_heat_pca | Man page |
| all_vivo_all_vitro | Man page Source code |
| append_break_labels | Man page |
| append_if_numeric | Man page |
| arrange_plots | Man page |
| arrange_poster | Man page |
| arrow_axis | Man page |
| arrow_to_graph | Man page |
| average_by_group | Man page |
| batch_correct | Man page |
| block_with_parameter | Man page Source code |
| break_time_line | Man page |
| cell_cycle | Man page |
| cell_heat | Man page |
| cell_violin | Man page |
| change_expre_level | Man page |
| clean_metadata | Man page |
| colony_count | Man page |
| colors2labels | Man page |
| compare_cluster_enrichment | Man page |
| compare_reactome | Man page |
| compute_all_cor | Man page |
| custom_color | Man page |
| custom_net | Man page |
| custom_net_diff_nets | Man page |
| custom_net_from_seurat | Man page Source code |
| custom_scale | Man page |
| custom_text | Man page |
| custom_text_str | Man page |
| custom_tick | Man page |
| cycle_over_time | Man page |
| data_timeline | Man page |
| date_to_CS | Man page |
| date_to_gene | Man page |
| determine_color_gradient | Man page |
| determine_power | Source code |
| dim_3_to_2 | Man page |
| dim_plot_cell_similarity | Man page |
| dim_red_3D | Man page |
| dim_red_3D_traj | Man page |
| display_cluster_enrichment | Man page |
| emap_graph_build | Source code |
| expand_length | Man page |
| fast_subset | Man page |
| filter_expression | Man page |
| filter_genes | Man page |
| find_DE_genes | Man page |
| find_DE_pairwise | Man page |
| find_eigengene | Man page |
| find_peak | Man page |
| find_transition_from_seurat | Man page |
| format_conf | Man page |
| frequency_plot | Man page |
| gene_gene_mat | Man page |
| gene_name_to_entrez | Man page |
| gene_over_pseudotime | Man page |
| gene_per_enriched_term | Man page |
| gene_per_term | Man page |
| get_DE_from_KL | Man page |
| get_all_path_view | Man page |
| get_arrow | Man page |
| get_cell_similarity | Man page |
| get_cycle_order | Source code |
| get_gene_list | Man page |
| get_gene_names | Man page |
| get_igraph | Source code |
| get_module_score | Man page |
| get_p | Source code |
| get_path | Man page |
| get_path_genes | Man page |
| get_pathway_view | Man page |
| get_phase_score | Man page |
| get_time_axis | Man page |
| get_y_union | Source code |
| gg_DimPlot | Man page |
| gg_bar | Man page |
| gg_plot_dim_red | Man page |
| gg_silva | Man page |
| graph_abs_time | Man page |
| hub_score | Man page |
| incorporate_TSC | Man page |
| integrated_seurat | Man page |
| label_transfer | Man page |
| lineage_markers | Man page |
| load_all_data | Man page |
| load_correct_label | Man page |
| make_anno_legend | Man page |
| make_cycle_heat | Man page |
| mat_to_seurat | Man page |
| mean_log_likelihood | Man page |
| merge_compareClusterResult | Source code |
| merge_seurat | Man page |
| mixed_order_sort | Man page |
| normalize_prob | Man page |
| p_val_all_pairs | Man page |
| partial_relevel | Man page |
| path_eigen | Man page |
| pathway_heat_pca | Man page |
| pca_with_pt_line | Man page |
| peak_gene_for_heatmap | Man page |
| phase_PC_plot | Man page |
| phase_density_plot | Man page |
| plot_BC_filter | Man page |
| plot_DE_genes | Man page |
| plot_WGCNA_net | Man page |
| plot_all_WGCNA_nets | Man page |
| plot_cell_similarity | Man page |
| plot_colony_count | Man page |
| plot_dendrogram | Source code |
| plot_dim_red | Man page |
| plot_gene_PC | Man page |
| plot_one_branch | Man page |
| plot_prob_line | Man page |
| plot_two_branch | Man page |
| prepare_pie_category | Source code |
| prepare_pie_data | Source code |
| preprocess | Man page |
| preprocess_df | Man page |
| print_dim | Man page |
| pseudo_real_time | Man page |
| pseudotime_heat | Man page |
| raw_to_seurat | Man page |
| remove_ribosomal_genes | Man page |
| rescaling | Man page |
| return_aes_param | Man page |
| rich_forest | Man page |
| ridge_all_types | Man page |
| ridge_one_type | Man page Source code |
| row_start_end_coord | Man page |
| run_GSEA | Man page |
| run_GSEA_all_types | Man page |
| run_GSEA_pairwise | Man page |
| run_dim_red | Man page |
| sagittae | Man page |
| save_DE_genes | Man page |
| save_DE_pairwise | Man page |
| save_for_10X | Man page |
| save_hub_score | Man page |
| save_indiv_plots | Man page |
| save_peak_genes | Man page |
| save_seurat | Source code |
| save_to_csv | Man page |
| scaling | Man page |
| selected_cell_PCA | Man page |
| seurat_heat | Man page |
| seurat_heat_highlight | Man page |
| seurat_heat_split | Man page |
| seurat_list_score | Man page |
| seurat_violin | Man page |
| seurat_volcano | Man page |
| sigmoid | Man page |
| signif_p_val | Man page |
| sim_emap | Man page Source code |
| sparsify | Man page |
| standardise_name | Man page |
| strong_gene_violin | Man page |
| subset_celltype | Man page |
| subset_terms | Man page |
| summarise_gsea | Man page |
| term_gene_labels | Man page |
| text_3D_repel | Man page |
| theme_TB | Man page |
| theme_dim_red | Man page |
| time_cluster_plot | Man page |
| unique_DE_genes | Man page |
| update_n | Source code |
| wrap_long_sentence | Man page |
| write_module_gene | Man page |
