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immReferent 1.0.2

New Features

  • Added OGRDB (AIRR Community) support with full suite of functions:
    • getOGRDB(): Download germline sets from OGRDB
    • loadOGRDB(): Load OGRDB sequences into environment
    • refreshOGRDB(): Update locally cached OGRDB sequences
    • listOGRDB(): List archived OGRDB germline set versions
    • is_ogrdb_available(): Check OGRDB service availability
  • Added export functions for popular immune repertoire analysis tools:
    • exportMiXCR(): Export sequences for MiXCR custom library building
    • exportTRUST4(): Export sequences for TRUST4 analysis
    • exportCellRanger(): Export sequences for 10x Cell Ranger VDJ reference
    • exportIgBLAST(): Export sequences for IgBLAST database creation
  • Export functions work with sequences from both IMGT and OGRDB sources
  • Redirected HLA-based queries to IPD-IMGT/HLA FTP site for improved reliability
  • Added support for additional species: cynomolgus monkey, pig, and dog

Documentation Improvements

  • Added package-level man page (immReferent-package)
  • Renamed getting-started vignette to immReferent and expanded content
  • Expanded caching vignette with additional guidance
  • Standardized roxygen2 documentation across all functions with proper formatting using \code{}, \strong{}, \itemize{}, and \url{}
  • Added comprehensive @seealso sections linking related functions
  • Improved parameter documentation with explicit type specifications
  • Added return value documentation to OGRDB functions
  • Added Bioconductor installation instructions to README and vignette

Infrastructure

  • Set up GitHub Actions CI (R-CMD-check on macOS, Windows, Ubuntu)
  • Added test coverage reporting via codecov
  • Added PR command workflows for /document and /style
  • CI now runs on main, master, and devel branches
  • Updated R version dependency from 4.2.0 to 4.5.0
  • Added spelling wordlist

Testing

  • Reorganized test suite: split monolithic test file into focused modules
    • test-mainIMGT.R, test-mainOGRDB.R, test-export.R
    • test-cache.R, test-dowload.R, test-utils.R
  • Added comprehensive unit tests for export, OGRDB, cache, download, and utility functions

Bug Fixes

  • Fixed typo in is_ogrdb_available() documentation (was incorrectly referencing IMGT)
  • Fixed BiocCheck findings from initial submission

immReferent 0.99.0

  • Initial release with IMGT sequence downloading, caching, and loading