Function reference • TSRexploreR

General Functions Functions for general processing workflow.
`tsr_explorer()`	TSRexploreR Class
`format_counts()`	Format Counts
`annotate_features()`	Annotate Features
`plot_threshold_exploration()`	Plot Threshold Exploration
`apply_threshold()`	Apply a threshold to TSSs or TSRs
`merge_samples()`	Merge Samples
`normalize_counts()`	Normalize TSS counts
`tss_clustering()`	TSS Clustering
TSS/TSR Metrics Functions to explore TSS and/or TSR metrics.
`associate_with_tsr()`	Associate TSSs
`mark_dominant()`	Mark Dominant
`tsr_metrics()`	TSR Metrics
`plot_tsr_metric()`	Plot TSR Metrics
BAM Processing Functions to import and process BAM files.
`G_correction()`	Correct G artifact
`import_bams()`	Import BAMs
`softclip_composition()`	Composition of Soft-clipped Bases
`softclip_histogram()`	Number of soft-clipped bases.
`tss_aggregate()`	Aggregate TSSs
TSS/TSR Import and Export Functions to import and export TSSs and TSRs.
`tss_import()`	Import TSSs
`tsr_import()`	Import TSRs
`tss_export()`	Export TSSs
`tsr_export()`	Export TSRs
Accessor Functions Functions to access data within TSRexploreR object.
`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
TSR Shifting Functions specific to TSR shifting analysis.
`tss_shift()`	TSS Shifting
`plot_shift_rank()`	Shifting Rank Plot
`plot_shift_count()`	Shift Count Plot
TSS/TSR Plotting Functions Plotting functions for TSS and TSR data.
`gene_tracks()`	Gene Tracks
`plot_correlation()`	Plot Sample Correlation
`plot_density()`	Density Plots
`plot_detected_features()`	Genes/Transcripts Detected
`plot_genomic_distribution()`	Genomic Distribution
`plot_heatmap()`	Plot Heatmap
`plot_reduction()`	Dimensionality Reduction.
TSS Specific Plots Plotting functions specific to TSS data.
`plot_dinucleotide_frequencies()`	Dinucleotide Analysis
`plot_sequence_colormap()`	Plot Sequence Color Map
`plot_sequence_logo()`	Generate Sequence Logo
Differential TSSs/TSRs Functions for differential TSS/TSR analysis and plotting.
`fit_de_model()`	Differential feature analysis
`differential_expression()`	Analyze Differential Features
`export_for_enrichment()`	Export to clusterProfiler
`plot_ma()`	MA Plot
`plot_num_de()`	Plot DE Numbers
`plot_volcano()`	Volcano Plot
Data Conditionals Accessory functions to condition data for plotting
`conditionals()`	Data Conditions Input
`ordering()`	Ordering
`quantiling()`	Quantiling
Datasets Internal datasets.
`TSSs`	Yeast STRIPE-seq TSSs
`TSSs_reduced`	STRIPE-seq TSSs YDR077W (Diamide)
Internal Functions Internal functions that should be ignored by end user
`ShiftScores()`	Shift Score
`common_params()`	Function to hold common parameters.
`.count_features()`	Calculate Feature Counts
`.count_matrix()`	Generate Count Matrix.
`.de_status()`	Mark DE Status
`.out_of_bounds_index()`	Get index of out of bounds ranges.
`.prepare_annotation()`	Prepare Genome Annotation
`.prepare_assembly()`	Prepare Genome Assembly
`condition_data()`	Data Conditionals
`extract_counts()`	Extract Counts
`extract_de()`	Extract Differential Gene Sets
`extract_matrix()`	Extract Count Matrices
`preliminary_filter()`	Preliminary Filter
`retrieve_seqs()`	Retrieve Sequences
`set_count_slot()`	Set Slot Data
`tsr_experiment()`	Add TSRs
`tss_experiment()`	Add TSSs

Reference

General Functions

TSS/TSR Metrics

BAM Processing

TSS/TSR Import and Export

Accessor Functions

TSR Shifting

TSS/TSR Plotting Functions

TSS Specific Plots

Differential TSSs/TSRs

Data Conditionals

Datasets

Internal Functions