Bioc review

[ncborcherding]

• 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.

  All issues based on: immGLIPH Bioconductor/Contributions#4143

[codecov]

Codecov Report

❌ Patch coverage is 78.20513% with 153 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
R/deNovoTCRs.R	64.86%	52 Missing ⚠️
R/clusterScoring.R	82.06%	40 Missing ⚠️
R/local-fisher.R	6.89%	27 Missing ⚠️
R/getRandomSubsample.R	85.71%	10 Missing ⚠️
R/plotNetwork.R	37.50%	10 Missing ⚠️
R/clustering.R	94.15%	9 Missing ⚠️
R/utils-input.R	0.00%	2 Missing ⚠️
R/global-cutoff.R	80.00%	1 Missing ⚠️
R/runGLIPH.R	97.29%	1 Missing ⚠️
R/utils-parallel.R	80.00%	1 Missing ⚠️

Files with missing lines	Coverage Δ
R/global-fisher.R	90.85% <100.00%> (-0.36%)	⬇️
R/local-rrs.R	91.48% <100.00%> (ø)
R/global-cutoff.R	98.16% <80.00%> (-0.05%)	⬇️
R/runGLIPH.R	90.72% <97.29%> (+0.01%)	⬆️
R/utils-parallel.R	88.88% <80.00%> (-11.12%)	⬇️
R/utils-input.R	79.48% <0.00%> (ø)
R/clustering.R	75.22% <94.15%> (-1.52%)	⬇️
R/getRandomSubsample.R	88.76% <85.71%> (-4.86%)	⬇️
R/plotNetwork.R	46.36% <37.50%> (+0.46%)	⬆️
R/local-fisher.R	62.85% <6.89%> (+11.29%)	⬆️
... and 2 more

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