Changes in version 0.99.5                        

  - Vignette: removed undefined variable references (mouse_tcr_data,
    contig_list placeholder, ... in custom_ref). Five previously
    unevaluated chunks now run during build, using tempdir(),
    scRepertoire::contig_list, the bundled gliph_sce, and a real
    reference data frame built from gliph_input_data. The three
    remaining eval = FALSE chunks are limited to BiocManager::install()
    calls and the optional getGLIPHreference() network download.
  - Consolidated duplicated column-type coercion for loops in
    loadGLIPH(), plotNetwork() and clusterScoring() into a single
    lapply()-based helper, .coerce_numeric_cols().

                       Changes in version 0.99.4                        

  - Added a Validation section to the README with concordance metrics
    against the published GLIPH and GLIPH2 cluster vectors from
    Glanville et al. (2017) and Huang et al. (2020). With paper-matched
    parameters, immGLIPH reproduces the published cluster vectors at
    ARI 0.985 (Glanville) and 0.863 (Huang) on the intersection of
    shared CDR3s. Full benchmark code lives at
    BorchLab/immGLIPH-benchmark.
  - Fixed clusterScoring() failure in the clonal-expansion-enrichment
    test when a cluster contains more members than the reference pool
    has rows. The null draw now uses replace = TRUE (bootstrap),
    matching the V-gene null and the statistically appropriate choice
    for resampling. Surfaced on the Huang 2020 benchmark.

                       Changes in version 0.99.3                        

  - Replaced foreach/doParallel with BiocParallel for parallelization
    across all functions per Bioconductor recommendations.
  - Replaced devtools::install_github() references with
    BiocManager::install() in vignette and error messages.
  - Updated vignette to use SingleCellExperiment instead of Seurat for
    the single-cell workflow example.
  - Fixed combineTCR() example in vignette (removed obsolete cells
    argument).
  - Made more vignette code chunks evaluable (clusterScoring(),
    deNovoTCRs(), plotNetwork() examples).
  - Noted that scRepertoire and immApex are Bioconductor packages.
  - Replaced iterative for-loop list growing with vectorized
    alternatives (lapply(), vapply(), Reduce()).
  - Standardized code spacing around operators and after commas per
    Bioconductor coding style.

                       Changes in version 0.99.2                        

  - Fixing roxygen documentation issue creating warnings.

                       Changes in version 0.99.1                        

  - Moved reference repertoire data hosting from GitHub releases to
    Zenodo (https://zenodo.org/records/18925758) per Bioconductor
    requirements.
  - Updated getGLIPHreference() to download from Zenodo.

                       Changes in version 0.99.0                        

  - Initial Bioconductor submission
  - R implementation of GLIPH and GLIPH2 algorithms for TCR clustering
  - Integration with scRepertoire ecosystem via immApex
  - Interactive network visualization with plotNetwork()
  - De novo TCR sequence generation with deNovoTCRs()