Changes in version 0.99.4                        

  - The README describes installation from Bioconductor, links the
    PscanRBackgrounds package page on Bioconductor, and gives the order
    in which ps_retrieve_bg() tries ExperimentHub and the Zenodo
    records.

                       Changes in version 0.99.3                        

  - Promoters of different lengths are not comparable, because a
    promoter's best motif score depends on its length. pscan(),
    pscan_filtered() and ps_build_bg() now keep the promoters of the
    most common length (before, those of the longest one), and the
    warning reports how many promoters were kept, their length, and how
    many were discarded.
  - pscan_filtered() removes duplicated promoters and promoters of other
    lengths, as pscan() does.
  - ps_scan() warns when it is called directly on promoters of different
    lengths, which it scans one at a time.
  - pscan(), pscan_filtered() and ps_build_bg() stop with an error that
    names the motifs when the promoters kept are shorter than any motif
    in the collection. Before, pscan() failed with an unrelated z-test
    error, pscan_filtered() with "logical subscript contains NAs", and
    ps_build_bg() silently stored NaN background statistics. ps_scan()
    stops with a clear error when no promoter is long enough for its
    motif.
  - pscan_filtered() encodes the promoters once for all motifs, as
    pscan() does.
  - Argument checks are shared by all exported functions and stop with
    one wording, such as "'x' must be a DNAStringSet", without showing
    internal function names. Checks that were missing are added:
    ps_retrieve_bg_from_file() requires a file path,
    ps_build_bg_from_table() a data.frame, ps_build_bg() a logical
    fullBG, and pscan_filtered() a numeric n. ps_write_bg_to_file()
    reports an output file or directory it cannot write to; the check
    existed but never ran. ps_motif_barplot() accepts an FDR only
    between 0 and 1, as ps_results_table() does.
  - Removed internal code without callers: .ps_natural_order(), the
    stored PSMatrixList class generator, and the .PS_PSEUDOCOUNT() and
    all_sequences_id() accessor generics (the latter read a slot that
    PSMatrix does not have).
  - Tests cover the per-sequence scanner used for promoters of different
    lengths.

                       Changes in version 0.99.2                        

  - Changes from the Bioconductor review:
      - ps_motif_barplot() and the density and hit-score plots use the
        Okabe-Ito colour-blind-safe palette from
        grDevices::palette.colors().
      - The vignettes locate their bundled files with system.file(), so
        every displayed chunk can be run as shown.
      - The funder is listed in Authors@R.
      - PscanRBackgrounds, the ExperimentHub package with the
        precomputed backgrounds, is in Suggests now that it is part of
        Bioconductor.
      - Minor code cleanup: no comparisons with TRUE, startsWith() for
        prefix tests, toString() for comma-separated lists.
      - The code follows a lintr configuration (.lintr: 4-space
        indentation, 80 columns) that CI enforces; the tests were
        reindented to match.
      - Consistent argument names: ps_retrieve_bg(jaspar_release = )
        (was JASPAR_matrix) and ps_scan(use_full_bg = ) (was
        use_full_BG).

                       Changes in version 0.99.0                        

  - Initial Bioconductor submission.
  - pscan() implements the Pscan method (Zambelli, Pesole and
    Pavesi, 2009, doi:10.1093/nar/gkp464): it tests a set of promoter
    sequences for transcription factor binding motifs that score higher
    than in a background of all promoters of the organism, and reports
    z-scores, p-values and FDR.
  - Precomputed backgrounds for the JASPAR 2020, 2022 and 2024 CORE
    collections, seven genome assemblies and five promoter windows are
    retrieved from ExperimentHub (package PscanRBackgrounds), or
    directly from their Zenodo records, with ps_retrieve_bg() and listed
    with ps_available_bg().
  - Custom backgrounds can be built with ps_build_bg() and saved and
    reloaded with ps_write_bg_to_file() and ps_retrieve_bg_from_file().
    Full backgrounds keep per-promoter hits, so that pscan_full_bg() can
    test a set of transcripts without rescanning sequences.
  - pscan_filtered() restricts an analysis to motifs that pass a first
    scan.
  - ps_select_promoters() and ps_selection_summary() choose one promoter
    per gene from a gene list.
  - Results are summarised with ps_results_table() and visualised with
    ps_zscore_heatmap(), ps_motif_barplot(), ps_density_plot(),
    ps_hitpos_map() and ps_hit_score_plot().
  - Motif scanning can run in parallel through BiocParallel; it is
    serial by default.