Changes in version 1.13.1                        

This release adds two new classification schemes (TAPscan and
Plant-TFClass) and redesigns the API around a simpler workflow:
annotate_domains() -> classify_tfs() -> get_tf_counts().

NEW FEATURES

  - TFs can now be classified using the classification scheme of TAPscan
    v4 (Petroll et al., 2025), in addition to PlantTFDB's scheme. The
    TAPscan classification algorithm (tapscan_classify.pl v4.76, with
    rules v82 and coverage values v11) was ported to R and reproduces
    the results of the original Perl implementation. TAPscan
    classifications include a variable TAP_class indicating whether each
    family contains transcription factors (TF), transcriptional
    regulators (TR), or putative TAPs (PT).

  - TFs are also classified into superclasses, classes, and families
    from the structure-based classification of Plant-TFClass
    (Blanc-Mathieu et al., 2024). Plant-TFClass classifications are
    inferred from TAPscan classifications using a correspondence table
    between the two systems. When a TAPscan subfamily corresponds to
    more than one Plant-TFClass family (TAPscan's AP2, ABI3/VP1, and
    MADS), PlantTFDB subfamilies are used to resolve the ambiguity; when
    that is not possible, all possible classifications are reported,
    separated by ';'.

  - PlantTFDB classifications now include both families (e.g., AP2/ERF)
    and subfamilies (e.g., ERF), as in PlantTFDB's classification
    scheme.

  - New function annotate_domains() to annotate sequences with the
    domains used by PlantTFDB and TAPscan. It has a threads argument to
    run HMMER with multiple threads.

  - New data sets tapscan_scheme (TAPscan's classification rules),
    planttfclass_scheme (correspondence between TAPscan and
    Plant-TFClass), and tap_class (classes, descriptions, and references
    for TAPscan families).

BREAKING CHANGES

  - annotate_pfam() was replaced by annotate_domains(), which returns a
    list of two data frames (PlantTFDB and TAPscan) with variables Gene,
    Domain, qlen, c_evalue, hmm_from, and hmm_to.

  - classify_tfs() now takes the output of annotate_domains() as input
    (data frames returned by annotate_pfam() are no longer accepted),
    and returns a data frame with one row per gene and variables Gene,
    PlantTFDB_family, PlantTFDB_subfamily, TAPscan_family,
    TAPscan_subfamily, TAP_class, PlantTFClass_superclass,
    PlantTFClass_class, and PlantTFClass_family. Note that the
    classifications previously reported in the variable Family (e.g.,
    ERF) are now in PlantTFDB_subfamily, and PlantTFDB_family contains
    PlantTFDB families (e.g., AP2/ERF). Genes assigned to more than one
    PlantTFDB family have families (and subfamilies) separated by ';'.

  - get_tf_counts() now takes a named list of data frames with TF
    classifications (as returned by classify_tfs()) as input, instead of
    a list of AAStringSet objects. This way, domains are annotated only
    once, and TFs can be counted in different ways (and filtered, if
    needed) without running HMMER again. By default, TFs are counted per
    PlantTFDB family (previously, PlantTFDB subfamily).

  - Data set classification_scheme was renamed to planttfdb_scheme, and
    names 'M_type', 'MYB_related', and 'LBD (AS2/LOB)' were changed to
    'M-type', 'MYB-related', and 'LBD', respectively, to match the
    output of classify_tfs().

  - Data sets gsu_families and tf_counts were removed, as they can be
    obtained in a few milliseconds with classify_tfs(gsu_annotation) and
    get_tf_counts(), respectively. Data sets gsu and gsu_annotation were
    updated.

BUG FIXES

  - HD-ZIP (via HD-ZIP_I/II), TALE (via BELL), and WOX TFs were never
    identified, because the names of these domains did not match the
    names of their profile HMMs. Such TFs were classified as HB-other.

  - Trihelix and STAT TFs were never identified for the same reason.

  - Genes with two B-box domains and a CCT domain were classified as
    both CO-like and DBB. They are now classified as CO-like only.

  - get_tf_counts() returned an error when species names were not in
    alphabetical order, and did not reorder species metadata to match
    the order of species in the count matrix.

                       Changes in version 0.99.2                        

CHANGES

  - Made small changes suggested by Bioconductor reviewer.

                       Changes in version 0.99.0                        

NEW FEATURES

  - Added a NEWS.md file to track changes to the package.