Man pages for zentnerlab/TSRexploreR
TSS and TSR Analysis
| annotate_features | Annotate Features |
| apply_threshold | Apply a threshold to TSSs or TSRs |
| associate_with_tsr | Associate TSSs |
| common_params | Function to hold common parameters. |
| conditionals | Data Conditions Input |
| condition_data | Data Conditionals |
| differential_expression | Analyze Differential Features |
| dot-count_features | Calculate Feature Counts |
| dot-count_matrix | Generate Count Matrix. |
| dot-de_status | Mark DE Status |
| dot-out_of_bounds_index | Get index of out of bounds ranges. |
| dot-prepare_annotation | Prepare Genome Annotation |
| dot-prepare_assembly | Prepare Genome Assembly |
| export_for_enrichment | Export to clusterProfiler |
| extract_counts-function | Extract Counts |
| extract_de-function | Extract Differential Gene Sets |
| extract_matrix-function | Extract Count Matrices |
| fit_de_model | Differential feature analysis |
| format_counts | Format Counts |
| G_correction | Correct G artifact |
| gene_tracks | Gene Tracks |
| get_annotation | Get Genome Annotation |
| get_assembly | Get Genome Assembly |
| get_counts | Get TSS or TSR count tables. |
| get_diff_model | Get Differential TSS/TSR models |
| get_diff_results | Get Differential TSS/TSR results |
| get_granges | Get TSS or TSR GRanges. |
| get_sample_sheet | Get Sample Sheet |
| get_shifting_results | Get Shifting Results |
| import_bams | Import BAMs |
| mark_dominant | Mark Dominant |
| merge_samples | Merge Samples |
| normalize_counts | Normalize TSS counts |
| ordering | Ordering |
| pipe | Pipe operator |
| plot_correlation | Plot Sample Correlation |
| plot_density | Density Plots |
| plot_detected_features | Genes/Transcripts Detected |
| plot_dinucleotide_frequencies | Dinucleotide Analysis |
| plot_genomic_distribution | Genomic Distribution |
| plot_heatmap | Plot Heatmap |
| plot_ma | MA Plot |
| plot_num_de | Plot DE Numbers |
| plot_reduction | Dimensionality Reduction. |
| plot_sequence_colormap | Plot Sequence Color Map |
| plot_sequence_logo | Generate Sequence Logo |
| plot_shift_count | Shift Count Plot |
| plot_shift_rank | Shifting Rank Plot |
| plot_threshold_exploration | Plot Threshold Exploration |
| plot_tsr_metric | Plot TSR Metrics |
| plot_volcano | Volcano Plot |
| preliminary_filter | Preliminary Filter |
| quantiling | Quantiling |
| retrieve_seqs | Retrieve Sequences |
| set_slot-function | Set Slot Data |
| ShiftScores-function | Shift Score |
| softclip_composition | Composition of Soft-clipped Bases |
| softclip_histogram | Number of soft-clipped bases. |
| tsr_experiment-generic | Add TSRs |
| tsr_explorer-class | TSRexploreR Class |
| tsr_export | Export TSRs |
| tsr_import | Import TSRs |
| tsr_metrics | TSR Metrics |
| tss_aggregate | Aggregate TSSs |
| tss_clustering | TSS Clustering |
| tss_experiment-generic | Add TSSs |
| tss_export | Export TSSs |
| tss_import | Import TSSs |
| TSSs | Yeast STRIPE-seq TSSs |
| tss_shift | TSS Shifting |
| TSSs_reduced | STRIPE-seq TSSs YDR077W (Diamide) |
