_pkgdown.yml

reference:
- subtitle: "General Functions"
  desc: "Functions for general processing workflow."
- contents:
  - tsr_explorer
  - format_counts
  - annotate_features
  - plot_threshold_exploration
  - apply_threshold
  - merge_samples
  - normalize_counts
  - tss_clustering
- subtitle: "TSS/TSR Metrics"
  desc: "Functions to explore TSS and/or TSR metrics."
- contents:
  - associate_with_tsr
  - mark_dominant
  - tsr_metrics
  - plot_tsr_metric
- subtitle: "BAM Processing"
  desc: "Functions to import and process BAM files."
- contents:
  - G_correction
  - import_bams
  - starts_with("softclip")
  - tss_aggregate
- subtitle: "TSS/TSR Import and Export"
  desc: "Functions to import and export TSSs and TSRs."
- contents:
  - tss_import
  - tsr_import
  - tss_export
  - tsr_export
- subtitle: "Accessor Functions"
  desc: "Functions to access data within TSRexploreR object."
- contents:
  - starts_with("get")
- subtitle: "TSR Shifting"
  desc: "Functions specific to TSR shifting analysis."
- contents:
  - tss_shift
  - plot_shift_rank
  - plot_shift_count
- subtitle: "TSS/TSR Plotting Functions"
  desc: "Plotting functions for TSS and TSR data."
- contents:
  - gene_tracks
  - plot_correlation
  - plot_density
  - plot_detected_features
  - plot_genomic_distribution
  - plot_heatmap
  - plot_reduction
- subtitle: "TSS Specific Plots"
  desc: "Plotting functions specific to TSS data."
- contents:
  - plot_dinucleotide_frequencies
  - plot_sequence_colormap
  - plot_sequence_logo
- subtitle: "Differential TSSs/TSRs"
  desc: "Functions for differential TSS/TSR analysis and plotting."
- contents:
  - fit_de_model
  - differential_expression
  - export_for_enrichment
  - plot_ma
  - plot_num_de
  - plot_volcano
- subtitle: "Data Conditionals"
  desc: "Accessory functions to condition data for plotting"
- contents:
  - conditionals
  - ordering
  - quantiling
- subtitle: "Datasets"
  desc: "Internal datasets."
- contents:
  - TSSs
  - TSSs_reduced
- subtitle: "Internal Functions"
  desc: "Internal functions that should be ignored by end user"
- contents:
  - ShiftScores
  - common_params
  - matches("^\\.")
  - condition_data
  - starts_with("extract")
  - preliminary_filter
  - retrieve_seqs
  - set_count_slot
  - tsr_experiment
  - tss_experiment