NEWS
immReferent 0.99.7
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