API for zentnerlab/TSRexploreR
TSS and TSR Analysis
| Global functions | |
|---|---|
| %>% | Man page |
| .aggr_scores | Source code |
| .annotate | Source code |
| .count_features | Man page |
| .count_matrix | Man page Source code |
| .de_status | Man page |
| .edger_model | Source code |
| .edger_normalize | Source code |
| .explore_thresholds | Source code |
| .filter_data | Source code |
| .merge_overlapping_TSSs | Source code |
| .order_data | Source code |
| .out_of_bounds_index | Man page Source code |
| .prepare_annotation | Man page Source code |
| .prepare_assembly | Man page Source code |
| .tss_heatmap | Source code |
| .tss_sequences | Source code |
| G_correction | Man page |
| ShiftScore | Source code |
| ShiftScoreFast | Source code |
| ShiftScores | Man page |
| TSSs | Man page |
| TSSs_reduced | Man page |
| allTheShiftScores | Source code |
| annotate_features | Man page Source code |
| apply_threshold | Man page |
| associate_with_tsr | Man page Source code |
| common_params | Man page Source code |
| condition_data | Man page Source code |
| conditionals | Man page Source code |
| differential_expression | Man page |
| export_for_enrichment | Man page Source code |
| extract_counts | Man page Source code |
| extract_de | Man page Source code |
| extract_matrix | Man page Source code |
| fit_de_model | Man page Source code |
| format_counts | Man page Source code |
| gene_tracks | Man page Source code |
| get_annotation | Man page Source code |
| get_assembly | Man page Source code |
| get_counts | Man page Source code |
| get_diff_model | Man page Source code |
| get_diff_results | Man page Source code |
| get_granges | Man page Source code |
| get_sample_sheet | Man page Source code |
| get_shifting_results | Man page Source code |
| import_bams | Man page Source code |
| mark_dominant | Man page Source code |
| merge_samples | Man page Source code |
| normalize_counts | Man page Source code |
| ordering | Man page Source code |
| plot_correlation | Man page Source code |
| plot_density | Man page Source code |
| plot_detected_features | Man page Source code |
| plot_dinucleotide_frequencies | Man page Source code |
| plot_genomic_distribution | Man page Source code |
| plot_heatmap | Man page |
| plot_ma | Man page Source code |
| plot_num_de | Man page Source code |
| plot_reduction | Man page Source code |
| plot_sequence_colormap | Man page |
| plot_sequence_logo | Man page |
| plot_shift_count | Man page Source code |
| plot_shift_rank | Man page Source code |
| plot_threshold_exploration | Man page |
| plot_tsr_metric | Man page Source code |
| plot_volcano | Man page Source code |
| preliminary_filter | Man page |
| quantiling | Man page Source code |
| retrieve_seqs | Man page Source code |
| set_count_slot | Man page Source code |
| shape_index | Source code |
| softclip_composition | Man page Source code |
| softclip_histogram | Man page |
| tsr_experiment | Man page |
| tsr_experiment,tsr_explorer-method | Man page |
| tsr_explorer | Man page Source code |
| tsr_explorer-class | Man page |
| tsr_export | Man page Source code |
| tsr_import | Man page |
| tsr_metrics | Man page Source code |
| tss_aggregate | Man page |
| tss_clustering | Man page Source code |
| tss_experiment | Man page |
| tss_experiment,tsr_explorer-method | Man page |
| tss_export | Man page Source code |
| tss_import | Man page Source code |
| tss_shift | Man page Source code |
