Changes in version 0.99.0                        

Bioconductor submission development line. It is not a Bioconductor
release. The released GitHub version remains 0.1.0 (tag v0.1.0,
unchanged). The package has no DOI.

  - Version 0.99.0, the pre-release version required for a first
    Bioconductor submission.
  - New postexport_data_from_se(): converts an already state-resolved
    SummarizedExperiment into a postexport_data object, exactly as
    postexport_data() would for the equivalent wide table.
      - Layout A: events as rows, destructive samples as columns, time
        and replicate in colData, and four assays N, N_s, C, C_s.
      - It does not pair libraries, normalise, convert rMATS output or
        infer inclusion/skipping.
      - SummarizedExperiment is now in Imports.
  - Vignette: "Introduction" and "Installation" sections, and a short
    SummarizedExperiment input section.
  - The example-data generation script is distributed as
    inst/scripts/generate_postexport_example.R. It reproduces the
    shipped example data exactly.

                        Changes in version 0.1.0                        

First public release, published as a GitHub software release. It is not
a Bioconductor release (Bioconductor is the intended future distribution
channel), and the interface may still evolve. The package has no DOI.

Scientific reference

  - The numerical core is ported verbatim from the frozen manuscript
    implementation.
      - Repository: bioinformatics-sannio/postexport-kinetics.
      - Tag manuscript-revision-v1.0, commit
        65c3b7368fb7686bfde3dab857f98c393bb534c5.
      - Archive of the frozen manuscript implementation (not of this
        package): doi:10.5281/zenodo.22944109.
  - Ported components:
      - four-state ODE model and transcription schedules;
      - trapezoidal interval balances;
      - covariance estimation, shrinkage, eigenvalue floor and
        propagation;
      - whitened NNLS fits of the full model (sigma_c >= 0) and the null
        model (sigma_c = 0);
      - the statistic T = max(0, RSS0 - RSS1) and the boundary rule;
      - Crank-Nicolson null trajectories;
      - the replicate-level generative bootstrap and the add-one
        p-value.
  - Regression tests compare the package with fixtures generated from
    the frozen tag, on macOS and on Linux CI.

Inference

  - postexport_data() and validate_postexport_data(): validated wide or
    long input. Missing states are errors, never zero-filled.
  - postexport_control(): numerical and inferential settings with the
    frozen defaults (B = 1999).
  - fit_postexport_model(): full and null fits with diagnostics.
  - test_postexport_conversion(): bootstrap test of sigma_c = 0 against
    sigma_c > 0, with boundary information and RNG metadata.
  - print() and summary() methods for all result classes.

Simulation and design diagnostics

  - simulate_postexport_kinetics(): the manuscript simulator, with:
      - transcriptional onset and a common intervention time;
      - the NONE, SHUTOFF and PSEUDO_SHUTOFF regimes;
      - replicate variability and the benchmark assay-noise presets.
  - check_operational_domain(): diagnostic comparison of a design with
    the manuscript's corrected factorial benchmark. It is not a
    calibration guarantee.

Batch analysis, multiple testing, ranking and plots

  - Multi-event calls run sequentially with per-event seeds. An
    unexpected error in one event is recorded as status "event_error".
  - adjust_postexport_pvalues(): explicit multiple-testing adjustment
    (Benjamini-Hochberg by default) over valid tests, with user-defined
    families. A single test is a family of size one.
  - rank_postexport_candidates(): exploratory prioritisation with the
    manuscript's composite score. It is not inferential.
  - as.data.frame() methods give tidy result tables with documented
    column roles.
  - plot() methods (ggplot2) for fits, tests, result sets, simulations
    and operational-domain checks.

Documentation and data

  - Vignette vignette("postexportKinetics").
  - Synthetic example data postexport_example and
    postexport_example_truth, with a long-format copy in inst/extdata.

Compatibility and checks

  - Declared minimum versions: R (>= 4.1.0), ggplot2 (>= 3.4.0),
    testthat (>= 3.1.7).
  - Continuous integration: R 4.1 and oldrel-1 on Linux; the current R
    release on Linux, macOS and Windows; the Linux frozen-reference
    regression gate.

Not yet available

  - Parallel execution.
  - rMATS input conversion.
  - Comparator methods.
  - SummarizedExperiment input.