API for CSOgroup/CALDER
CALDER: a Hi-C non-linear hierarchical organization analysis tool
| Global functions | |
|---|---|
| CALDER | Man page |
| CALDER-package | Man page |
| CALDER_CD_hierarchy | Source code |
| CALDER_main | Source code |
| CALDER_sub_domains | Source code |
| Change.Point | Source code |
| Convert.Bin.To.Domain | Source code |
| Convert.Bin.To.Domain.TMP | Source code |
| Data.Norm | Source code |
| Detect.Local.Extreme | Source code |
| Get.Diamond.Matrix | Source code |
| Get.Diamond.Matrix2 | Source code |
| Get.Downstream.Triangle | Source code |
| Get.Pvalue | Source code |
| Get.Upstream.Triangle | Source code |
| HRG_MLE_each_compartment_fun | Source code |
| HRG_zigzag_compartment_domain_main_fun | Source code |
| HighResolution2Low | Source code |
| HighResolution2Low_k | Source code |
| HighResolution2Low_k_complete | Source code |
| HighResolution2Low_k_rectangle | Source code |
| LikelihoodRatioTest | Source code |
| MoC | Source code |
| PC_compartment | Source code |
| PC_compartment_slim | Source code |
| TopDom_v2 | Source code |
| Which.Gap.Region | Source code |
| Which.Gap.Region2 | Source code |
| Which.Gap.Region3 | Source code |
| Which.process.region | Source code |
| add_boundary_binsignal_to_decrated_branches | Source code |
| adjust_hs | Source code |
| bisecting_kmeans | Source code |
| build_chr_bin_domain_fun | Source code |
| build_chr_bin_domain_fun_direct | Source code |
| clean_TADs_all | Source code |
| compress_mat_fast | Source code |
| compress_mat_fast_tmp | Source code |
| compute_L | Source code |
| contact_mat_processing | Source code |
| correct_A_fast_divide_by_mean | Source code |
| correct_A_fast_equal_mean | Source code |
| creat_phylo_object | Source code |
| create_TADs | Source code |
| create_compartment_bed_v4 | Source code |
| densplot | Source code |
| dist_max_min | Source code |
| divide_into_groups | Source code |
| fast_cor | Source code |
| fast_cor_cor | Source code |
| fit_lnorm | Source code |
| generate_compartment_segs | Source code |
| generate_compartments_bed | Source code |
| generate_hierachy_bed | Source code |
| get_A_len | Source code |
| get_A_ln1 | Source code |
| get_A_ln2 | Source code |
| get_PCs | Source code |
| get_adjusted_nested_TADs | Source code |
| get_all_tads_in_a_trimmed_branch | Source code |
| get_best_reorder | Source code |
| get_bin_singals_CHiP | Source code |
| get_ccA_atanh | Source code |
| get_cluser_assignment | Source code |
| get_cluser_levels | Source code |
| get_cluster_bin_names | Source code |
| get_cluster_boudaries | Source code |
| get_cluster_index | Source code |
| get_clusters_bins_xy | Source code |
| get_corner_xy | Source code |
| get_detailed_full_tree | Source code |
| get_gene_info | Source code |
| get_half_mat_values | Source code |
| get_half_mat_values_v2 | Source code |
| get_hkmeans_cluser_levels | Source code |
| get_least_residue_matrix | Source code |
| get_leaves | Source code |
| get_level_k_TADs | Source code |
| get_level_k_nodes | Source code |
| get_original_tad_indices | Source code |
| get_original_tad_indices_extra | Source code |
| get_segments | Source code |
| get_stair_vecs | Source code |
| get_tree_decoration | Source code |
| get_tree_v0 | Source code |
| imputation_list | Source code |
| insulation_score_fun | Source code |
| is_binary_tree | Source code |
| join_left_or_right | Source code |
| loglik_lnorm_cpp | Source code |
| loglik_lnorm_cpp_mat | Source code |
| loglik_lnorm_cpp_vec | Source code |
| lognormal_mean_test | Source code |
| long_slices | Source code |
| mat_10to40kb | Source code |
| mat_split_sum | Source code |
| matrix_multiplication_cpp | Source code |
| matrix_multiplication_sym_cpp | Source code |
| matsplitter_sum | Source code |
| my_dist | Source code |
| my_kmeans | Source code |
| my_merge | Source code |
| n_cells2compute | Source code |
| p_likelihood_ratio | Source code |
| p_likelihood_ratio_gamma | Source code |
| p_likelihood_ratio_lnorm | Source code |
| p_likelihood_ratio_nb | Source code |
| p_likelihood_ratio_norm | Source code |
| p_lognormal_mean | Source code |
| p_wilcox_test | Source code |
| p_wilcox_test_nested | Source code |
| plot_tree | Source code |
| post_process_sub_domains | Source code |
| project_to_major_axis | Source code |
| prunning | Source code |
| prunning_bottom_up | Source code |
| prunning_hybrid | Source code |
| remove_blank_cols | Source code |
| remove_small_domains | Source code |
| reorder_dendro | Source code |
| rm_zeros | Source code |
| sim.fun | Source code |
| split_info | Source code |
| tree_germination | Source code |
| trim_tree_adaptive | Source code |
| trim_tree_adaptive_binsig_thresh | Source code |
| trim_tree_adaptive_bottom_up | Source code |
| trim_tree_adaptive_top_down_v2 | Source code |
| trim_tree_adaptive_width_thresh | Source code |
| update_branch_name | Source code |
| visualize_left_or_right | Source code |
| xenocraft | Source code |
| zigzag_loglik_ancestors_v4_5 | Source code |
