NEWS

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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