NEWS
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