API for snikumbh/seqArchR
Identify Different Architectures of Sequence Elements
| Global functions | |
|---|---|
| .add_check_range_outliers | Source code |
| .adjustSampleMemberships | Source code |
| .assert_seqArchR_NMFresult | Source code |
| .assert_seqArchR_OK_for_nextIteration | Source code |
| .assert_seqArchR_chunkSize_in_tandem | Source code |
| .assert_seqArchR_chunkSize_independent | Source code |
| .assert_seqArchR_collation | Source code |
| .assert_seqArchR_config | Source code |
| .assert_seqArchR_consistent_nSeqs_w_clusters | Source code |
| .assert_seqArchR_featSampMatrix | Source code |
| .assert_seqArchR_flags | Source code |
| .assert_seqArchR_globClustAssignments | Source code |
| .assert_seqArchR_kFolds_in_tandem | Source code |
| .assert_seqArchR_list_properties | Source code |
| .assert_seqArchR_min_size_in_tandem | Source code |
| .assert_seqArchR_min_size_independent | Source code |
| .assert_seqArchR_model_selection_params | Source code |
| .assert_seqArchR_nRuns | Source code |
| .assert_seqArchR_parallelization_params | Source code |
| .assert_seqArchR_seqsClustLabels | Source code |
| .assert_seqArchR_seqsClustLabels_at_end | Source code |
| .assert_seqArchR_thresholdIteration | Source code |
| .assert_seqArchRresult | Source code |
| .assert_seq_attributes | Source code |
| .assign_samples_to_clusters | Source code |
| .check_and_uncollate_siblings | Source code |
| .check_gtZero | Source code |
| .check_list_prop | Source code |
| .check_no_mag_change_fail_condition | Source code |
| .check_null_num | Source code |
| .compare_clusters | Source code |
| .compare_iqr_or_range | Source code |
| .compare_size | Source code |
| .compute_factor_distances | Source code |
| .compute_q2 | Source code |
| .cv_model_select_pyNMF2 | Source code |
| .decide_process_outer_chunk | Source code |
| .detect_overfitting | Source code |
| .form_ohe | Source code |
| .generate_folds | Source code |
| .get_amari_from_featMatList | Source code |
| .get_best_K | Source code |
| .get_cluster_memberships_per_run | Source code |
| .get_clusters_from_hc_using_cutree | Source code |
| .get_clusts_sil_or_ch | Source code |
| .get_factors_from_factor_clustering2 | Source code |
| .get_feat_names | Source code |
| .get_feat_or_samp_matList | Source code |
| .get_hopach_dist | Source code |
| .get_parent_chunks | Source code |
| .get_q2_aggregates_chosen_var | Source code |
| .get_q2_threshold_by_K | Source code |
| .get_q2_using_py | Source code |
| .get_stats_dist | Source code |
| .grid_srch_par_df | Source code |
| .handle_chunk_w_NMF2 | Source code |
| .handle_clustering_of_factors | Source code |
| .msg_print | Source code |
| .msg_pstr | Source code |
| .msg_range | Source code |
| .onLoad | Source code |
| .one_hot_encode | Source code |
| .perform_multiple_NMF_runs | Source code |
| .perform_single_NMF_run | Source code |
| .plot_cv_K | Source code |
| .prepare_chunks | Source code |
| .regularizeMat | Source code |
| .seqs_to_mat | Source code |
| .setup_clustFactors_for_seqArchR_result | Source code |
| .stability_model_select_pyNMF2 | Source code |
| .unfurl_nodeList | Source code |
| .update_cluster_labels | Source code |
| add_lims_lab | Source code |
| add_pseudo_count | Source code |
| amariDistance | Source code |
| check_cowplot | Source code |
| check_names_params | Source code |
| check_vars | Source code |
| check_vars2 | Source code |
| collapse_into_sinuc_matrix | Source code |
| collate_clusters | Man page Source code |
| collate_seqArchR_result | Man page Source code |
| computeAmariDistances | Source code |
| decisionToCollate | Source code |
| fetch_cutree_by_hc_order | Source code |
| fix_coord | Source code |
| get_clBasVec | Man page Source code |
| get_clBasVec_k | Man page Source code |
| get_clBasVec_m | Man page Source code |
| get_dimers_from_alphabet | Source code |
| get_features_matrix | Source code |
| get_ggheatmap | Source code |
| get_ggseqlogo | Source code |
| get_n_seeds | Source code |
| get_one_hot_encoded_seqs | Man page Source code |
| get_samples_matrix | Source code |
| get_seqClLab | Man page Source code |
| get_seqs_clust_list | Man page Source code |
| get_trimers_from_alphabet | Source code |
| handle_dir_creation | Source code |
| handle_only_neg_ticks | Source code |
| handle_only_pos_ticks | Source code |
| handle_pdffile_plotlist | Source code |
| handle_pdffile_plotting | Source code |
| intermediateResultsPlot | Source code |
| keepMinClusters | Source code |
| make_PWMs | Man page Source code |
| make_matrix | Source code |
| make_plot_title_str | Source code |
| make_plot_titles | Source code |
| manage_o_dir | Source code |
| performSearchForK | Source code |
| perform_setup | Source code |
| plot_all_seqs_logo | Source code |
| plot_arch_for_clusters | Man page Source code |
| plot_ggseqlogo_of_seqs | Man page Source code |
| prepare_data_from_FASTA | Man page Source code |
| process_innerChunk | Source code |
| save_checkpoint | Source code |
| save_final_result | Source code |
| scale_matrix | Source code |
| seqArchR | Man page Source code |
| seqs_str | Man page Source code |
| set_config | Man page Source code |
| set_default_pos_lab | Source code |
| set_default_pos_lab2 | Source code |
| set_ratio | Source code |
| set_xtick_labels | Source code |
| show_ellapsed_time | Source code |
| viz_bas_vec | Man page Source code |
| viz_pwm | Man page Source code |
| viz_seqs_acgt_mat | Man page Source code |
