Global functions | |
---|---|
.add_check_range_outliers | Source code |
.adjustSampleMemberships | Source code |
.assert_archR_NMFresult | Source code |
.assert_archR_OK_for_nextIteration | Source code |
.assert_archR_chunkSize_in_tandem | Source code |
.assert_archR_chunkSize_independent | Source code |
.assert_archR_collation | Source code |
.assert_archR_config | Source code |
.assert_archR_consistent_nSeqs_w_clusters | Source code |
.assert_archR_featuresMatrix | Source code |
.assert_archR_flags | Source code |
.assert_archR_globClustAssignments | Source code |
.assert_archR_kFolds_in_tandem | Source code |
.assert_archR_kFolds_independent | Source code |
.assert_archR_list_properties | Source code |
.assert_archR_min_size_in_tandem | Source code |
.assert_archR_min_size_independent | Source code |
.assert_archR_model_selection_params | Source code |
.assert_archR_nRuns | Source code |
.assert_archR_parallelization_params | Source code |
.assert_archR_samplesMatrix | Source code |
.assert_archR_seqsClustLabels | Source code |
.assert_archR_seqsClustLabels_at_end | Source code |
.assert_archR_thresholdIteration | Source code |
.assert_archRresult | Source code |
.assert_seq_attributes | Source code |
.assign_samples_to_clusters | Source code |
.check_and_uncollate_siblings | Source code |
.check_no_mag_change_fail_condition | Source code |
.compare_clusters | Source code |
.compare_iqr | Source code |
.compare_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_just_for_sake_clust | Source code |
.detect_overfitting | Source code |
.generate_folds | Source code |
.getMeanOfListOfMatrices | 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_modNW_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_q2_using_py_serial | 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_decode | Source code |
.one_hot_encode_dinuc | Source code |
.one_hot_encode_sinuc | Source code |
.one_hot_encode_trinuc | 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_archR_result | Source code |
.setup_par_cluster | Source code |
.stability_model_select_pyNMF2 | Source code |
.unfurl_nodeList | Source code |
.update_cluster_labels | Source code |
add_lims_lab | Source code |
amariDistance | Source code |
archR | Man page Source code |
archR_set_config | Man page Source code |
check_cowplot | Source code |
check_names_params | Source code |
check_par_conditions | Source code |
check_vars | Source code |
check_vars2 | Source code |
collapse_into_sinuc_matrix | Source code |
collate_archR_result | Man page Source code |
collate_clusters | 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_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 | Man page Source code |
intermediateResultsPlot | Source code |
keepMinClusters | Source code |
make_dinuc_PWMs | Man page Source code |
make_plot_title_str | Source code |
make_plot_titles | Source code |
make_sinuc_PWMs | Man page 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_ggheatmap | Man page Source code |
plot_ggseqlogo | Man page Source code |
plot_ggseqlogo_of_seqs | Man page Source code |
prepare_data_from_FASTA | Man page Source code |
process_innerChunk | Source code |
run_archR_UI | Man page Source code |
save_checkpoint | Source code |
save_final_result | Source code |
seqs_str | 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_heatmap | Man page Source code |
viz_bas_vec_heatmap_seqlogo | Man page Source code |
viz_bas_vec_seqlogo | Man page Source code |
viz_seqs_acgt_mat_from_seqs | Man page Source code |
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