Changes in version 1.3.3 (2026-09-28)                  

  - RN_iso_calc and RNentropy_iso_switch no longer return res, which
    duplicated gene_status and pv.
  - The default gene-level threshold of RN_iso_select (gene_pv) is
    now 0.05 (previously 0.01).
  - Corrected the package citation, which now lists the 2018 Nucleic
    Acids Research article and the 2021 Methods in Molecular Biology
    chapter.
  - Corrected and completed several help pages: an overview of both
    analyses in the package help, the exact testability rule of
    min_expr, cross-references between the isoform-switch functions,
    fixes to the dataset descriptions, and removal of outdated copies of
    the source code from the examples.

                        Changes in version 1.3.2                        

  - RN_iso_select now combines the sample p-values of each TESTED gene
    into a gene-level p-value with the Simes method and compares it with
    the threshold, without correction across genes. The threshold
    argument lpv_t is renamed gene_pv, the method argument and the
    lpv_adj component are removed, and the gene-level p-values are
    returned as gene_pv. selected reports the gene-level p-value
    (ISO_GENE_PV) next to the uncorrected per-sample p-values.
  - RN_iso_calc and RNentropy_iso_switch return the per-sample p-values
    as pv (formerly lpv), with columns named ISO_PV_<sample> (formerly
    ISO_LPV_<sample>).
  - Renamed the sample columns of RN_IsoSwitch_Example_S7 and of the
    compact S7 example file to plain tissue names (brain, heart, kidney,
    liver, lung, muscle).

                        Changes in version 1.3.1                        

  - Added RN_iso_select to apply multiple-testing correction to
    isoform-switch local p-values and retain genes significant in at
    least one sample.
  - Added runnable file-based examples for the standard and
    isoform-switch workflows using a shared synthetic regression
    dataset.

                        Changes in version 1.3.0                        

  - Initialized the public GitHub development repository from the
    verified CRAN 1.2.3 release.
  - Added continuous integration and repository provenance metadata.
  - Added RN_iso_calc and RNentropy_iso_switch for the analysis of
    isoform switching, with explicit testability information and results
    validated against the independent C++ implementation.
  - Added the complete historical S7 isoform-switch example as the
    compressed RN_IsoSwitch_Example_S7 package dataset.

                 Changes in version 1.2.3 (2022-04-13)                  

  - Fixed small bug in .RN_design_check preventing compatibility with R
    >=4.2.0
  - Added reference to new publication
  - Removed unneeded initialization of .Random.seed
  - Fixed a few typos in the documentation
  - Added README.md, NEWS.md, and cran-comments.md files