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NEWS.md

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immLynx 0.99.4

  • Added \value section to TCR_summary-class documentation to resolve R CMD check warning about empty/missing \value sections

immLynx 0.99.3

  • Addressed Bioconductor reviewer feedback
  • Updated R dependency to >= 4.6.0
  • Converted TCR_summary from S3 class to formal S4 class with show method
  • Added ORCID to Authors@R
  • Replaced \dontrun{} with \donttest{} in all examples except runSoNNia (kept as \dontrun{} due to upstream soNNia/numpy incompatibility)
  • Removed redundant tryCatch/stop() pattern in huggingModel(); replaced with on.exit() cleanup
  • Extracted shared .run_in_basilisk() helper to reduce code repetition across calculate.* functions
  • Added @importFrom SummarizedExperiment colData and removed explicit :: qualifiers in runOLGA, runClustTCR, and runEmbeddings
  • Added n == 0L edge-condition guard for seq.int() in proteinEmbeddings()
  • Expanded vignette introductions with biological context and detailed prose descriptions for each code section
  • Removed GitHub installation instructions from vignettes
  • Added additional unit tests for S4 class structure, edge cases, and input validation

immLynx 0.99.2

  • Removed the umbrella roxygen block from R/utils.R
  • Added skip_on_bioc_build() check directly inside skip_if_no_python() in tests/testthat/helper-immLynx.R

immLynx 0.99.1

  • Switched example data from Seurat to SingleCellExperiment object
  • Replaced Seurat with scran/scater in vignettes
  • Removed Seurat dependency; functions now use SingleCellExperiment exclusively
  • Renamed return_seurat parameter to return_input in runMetaclonotypist()

immLynx 0.99.0

  • Initial Bioconductor submission
  • Added runClustTCR() for TCR clustering via clusTCR
  • Added runTCRdist() for pairwise TCR distance calculations
  • Added runOLGA() and generateOLGA() for generation probability
  • Added runEmbeddings() for protein language model embeddings
  • Added runMetaclonotypist() for metaclone discovery
  • Added runHLAassociation() for HLA-metaclone associations
  • Added runSoNNia() for selection inference
  • Added utility functions: extractTCRdata(), validateTCRdata(), convertToTcrdist(), summarizeTCRrepertoire()
  • Added huggingModel(), tokenizeSequences(), and proteinEmbeddings() for custom embedding workflows