API for Kalhor-Lab/QFM
Quantitative Fate Mapping with ICE-FASE and Phylotime
| Global functions | |
|---|---|
| add_edge_length | Man page |
| adjust_pec_v1 | Source code |
| as.phylo | Source code |
| as.phylo.type_graph | Man page Source code |
| assign_node_states | Source code |
| backward_merge_sequence | Source code |
| barcode_allele_onehot | Source code |
| barcode_allele_onehot_new | Source code |
| build_constraint_matrices | Source code |
| bulk_to_sc | Source code |
| calc_bsum | Man page |
| calculate_type_counts | Man page Source code |
| calculate_type_counts_mod2 | Source code |
| calculate_type_counts_new | Source code |
| cells_to_edges | Man page |
| cells_to_nodes | Man page |
| change_target_time | Man page Source code |
| check_n_identity | Man page |
| check_type_count_seq | Source code |
| clr | Source code |
| collapse_reucr_ver | Source code |
| collaspe_di | Man page Source code |
| collect_edges | Source code |
| collect_nodes | Source code |
| compute_allele_prob | Source code |
| compute_loglike | Source code |
| compute_tree_loglike | Source code |
| concat_mut_p | Man page Source code |
| concat_mut_p_list | Man page Source code |
| construct_true_lineage_multi | Man page |
| correct_gr_edge_len | Source code |
| correct_trans_time | Source code |
| custom_dist | Source code |
| default_dist | Source code |
| distribute_all_mut_counts | Man page Source code |
| distribute_barcodes | Source code |
| distribute_mode_counts | Source code |
| distribute_mode_counts_mod2 | Source code |
| distribute_mut_counts | Man page Source code |
| distribute_sample_size | Source code |
| double_barcodes | Source code |
| double_mut_counts | Source code |
| dropout_sc_random | Source code |
| dump_mut_p | Source code |
| dump_mut_p_list | Source code |
| dump_sc_mat | Source code |
| dump_tr | Source code |
| dump_trees | Source code |
| edges_df_to_newick | Man page |
| est_func_case1 | Source code |
| est_func_case1a | Source code |
| est_func_case2 | Source code |
| est_transition_time | Source code |
| est_transition_time_multi | Source code |
| estimate_coal_time | Source code |
| eval_phy | Source code |
| evaluate_exp_node_assign | Source code |
| evaluate_experiment | Source code |
| evaluate_gr_res | Source code |
| evaluate_node_assign | Source code |
| evaluate_qfm_v1 | Source code |
| evalute_gr | Source code |
| evalute_gr_temp | Source code |
| evalute_gr_topo | Source code |
| extract_allele_matrix | Source code |
| fate_to_str | Source code |
| filter_allele_matrix | Source code |
| filter_allele_onehot | Source code |
| filter_cells | Source code |
| filter_noise_spacers | Source code |
| forward_merge_sequence | Source code |
| generate_control | Source code |
| generate_diff_outcome | Man page Source code |
| generate_edge_df | Man page Source code |
| generate_evaluate_tb | Source code |
| generate_gen_cell_id | Source code |
| generate_mut_color | Source code |
| generate_mut_ids | Man page Source code |
| generate_nonrecur_mut_ids | Man page Source code |
| generate_recur_mut_ids | Man page Source code |
| generate_recur_mut_ver_ids | Source code |
| generate_sample_size | Source code |
| get_barcodes | Source code |
| get_cell_type_counts | Man page Source code |
| get_dmat | Source code |
| get_edge_diff | Man page Source code |
| get_edge_len | Man page Source code |
| get_gr_progenitors | Source code |
| get_mode_counts | Source code |
| get_mrca_graph | Source code |
| get_mut_duration | Man page Source code |
| get_mutated_frac | Source code |
| get_new_muts | Source code |
| get_new_muts_barcode | Source code |
| get_next | Man page |
| get_node_mapping | Man page Source code |
| get_node_mapping_mod2 | Source code |
| get_node_seq | Source code |
| get_node_size | Source code |
| get_node_time | Source code |
| get_parent_node | Source code |
| get_parent_node_from_edges | Source code |
| get_parent_split_index | Source code |
| get_parent_split_index_mod2 | Source code |
| get_sample_size | Man page |
| get_sampled_cells | Man page |
| get_t_total | Man page Source code |
| get_target_time | Man page |
| get_tip_sample_size | Source code |
| get_trans_assign_tb | Source code |
| get_transitions | Source code |
| get_true_diff_time | Source code |
| get_true_sample_size_mod2 | Source code |
| get_true_size_mod2 | Man page |
| get_type_from_id | Source code |
| gr_color | Source code |
| hello | Man page |
| ice_fase | Man page Source code |
| ice_fase_multi | Source code |
| ice_fase_mutlifurc | Source code |
| impute_characters | Man page |
| init_cell_barcode | Source code |
| init_mut_counts_list | Man page Source code |
| initial_states_list | Man page Source code |
| initialize_mut_element_counter | Man page Source code |
| initialize_mut_state | Man page Source code |
| is_non_decs | Man page Source code |
| is_zero_range | Man page Source code |
| list_dd_and_tips | Source code |
| load_exp_data | Source code |
| load_sc_recon | Source code |
| load_true_sampled_sizes | Source code |
| log_choose | Source code |
| loglike_func_case1 | Source code |
| loglike_func_case2 | Source code |
| make_cell_type_gens | Source code |
| make_cell_type_gens_mod2 | Source code |
| make_edge_tb | Source code |
| make_gens | Source code |
| make_gens_mod2 | Source code |
| make_gr_tr_data | Man page Source code |
| make_gr_tr_data_mod2 | Source code |
| make_graph_from_phy_mod2 | Source code |
| make_heatmap_col | Man page Source code |
| make_ig_from_tr | Source code |
| make_merge_sequences | Source code |
| make_mut_element | Man page Source code |
| make_mut_param_by_rate | Man page Source code |
| make_mut_param_by_rate_rvec | Man page Source code |
| make_recur_vec_list | Source code |
| make_tree_data | Source code |
| make_true_gr_data | Source code |
| make_true_gr_data_mod2 | Source code |
| make_type_graph | Man page Source code |
| map_gr_label | Source code |
| mean_top_half | Source code |
| merge2phylo | Source code |
| merge_id_counts | Source code |
| merge_id_spacer_counts | Source code |
| merge_node_size | Source code |
| merge_sample_size | Source code |
| merge_spacer_counts | Source code |
| mut_counts_total | Man page Source code |
| mutate_barcodes | Man page Source code |
| mutate_cells | Man page Source code |
| name_nodes | Source code |
| next_cell_type_gens | Source code |
| node_label_mapper | Source code |
| normalize_row | Man page Source code |
| normalize_tree | Man page |
| num_gen_single_type | Man page Source code |
| offspring_mat | Source code |
| output_estimates | Source code |
| perturb_celltypes | Source code |
| phylotime | Man page |
| plot_barcodes | Source code |
| plot_col_vec | Man page Source code |
| plot_gr_data | Man page |
| plot_gr_data_mod1 | Source code |
| plot_gr_dendro | Source code |
| plot_ice_times | Source code |
| plot_legend | Man page |
| plot_node_sizes | Source code |
| plot_topology | Source code |
| plot_tr | Source code |
| plot_type_graph | Man page Source code |
| plot_type_graph_clean | Source code |
| plot_type_graph_clean_mod2 | Source code Source code |
| plot_type_graph_dendro | Source code |
| preproccess_tr | Source code |
| process_node_size | Source code |
| process_split_ratio | Source code |
| produce_dist | Source code |
| produce_phy | Source code |
| push_pdf | Man page Source code |
| push_png | Man page Source code |
| read_cassiopeia_tree | Source code |
| read_id_counts | Source code |
| read_id_spacer_counts | Source code |
| reconstruct_graph | Source code |
| reconstruct_graph_multi | Source code |
| remove_allele_ver | Source code |
| remove_uniform_id | Source code |
| round_frac | Source code |
| rstoc | Man page Source code |
| run_experiment | Source code |
| run_ice_fase | Source code |
| sample_all_barcodes | Source code |
| sample_all_barcodes_v1 | Source code |
| sample_all_mut_counts | Man page Source code |
| sample_all_mut_counts_gen | Man page Source code |
| sample_doublet_branch | Man page Source code |
| sample_doublet_twotype | Man page Source code |
| sample_mut_counts | Man page Source code |
| sample_mut_history_gens | Source code |
| sample_mut_num | Source code |
| sample_node_ranking | Source code |
| sample_sc_mut_history_gens | Source code |
| sample_size_gens | Source code |
| sc_to_bulk | Source code |
| scale_counts | Man page Source code |
| scale_min_max | Source code |
| score_single_element | Source code |
| set_color_palette | Source code |
| sim_history_to_edges | Man page |
| sim_history_to_nodes | Man page |
| simplify_edges_df | Man page |
| simulate_bulk | Source code |
| simulate_muts | Source code |
| simulate_parallel | Source code |
| simulate_sc_data | Source code |
| simulate_sc_muts | Source code |
| split_barcodes | Source code |
| split_mut_counts | Source code |
| strip_recur_ver | Source code |
| subsample_all_mut_counts | Man page Source code |
| subsample_mut_counts | Man page Source code |
| subset_mut_p | Man page Source code |
| transition2dist | Source code |
| update_edge_tb_state | Source code |
| update_gr_trans_time | Source code |
| update_tree_edge_len | Source code |
| white_col_mapper | Man page |
