NEWS

immGLIPH 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().

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.

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.

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