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Merged
ncborcherding merged 5 commits into from
Jan 4, 2026
Merged

Export functionality #11

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06d6f0e
export functions
ncborcherding Jan 4, 2026
b6c1a17
OGRDB export support
ncborcherding Jan 4, 2026
d0e191a
Update test-mainOGRDB.R
ncborcherding Jan 4, 2026
412616a
remove message testing
ncborcherding Jan 4, 2026
2d6a733
remove snapshot check
ncborcherding Jan 4, 2026
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14 changes: 10 additions & 4 deletions DESCRIPTION
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Package: immReferent
Title: An Interface for Immune Receptor and HLA Gene IMGT Reference Data
Version: 0.99.5
Title: An Interface for Immune Receptor and HLA Gene Reference Data
Version: 1.0.1
Authors@R: c(
person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"))
Description: Provides a consistent interface for downloading, storing, and accessing IMGT immune receptor (TCR/BCR) and HLA sequences (both nucleotide and protein). This package serves as a core dependency for immunogenomics packages, ensuring reliable and high-quality sequence access.
Description: Provides a consistent interface for downloading, storing, and
accessing immune receptor (TCR/BCR) and HLA sequences from IMGT,
IPD-IMGT/HLA, and OGRDB (AIRR-C). Supports export to popular analysis
tools including MiXCR, TRUST4, Cell Ranger, and IgBLAST. This package
serves as a core dependency for immunogenomics packages, ensuring
reliable and high-quality sequence access with local caching for
reproducibility.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2
RoxygenNote: 7.3.3
biocViews: Software, Annotation, Sequencing
Depends:
R (>= 4.5.0)
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4 changes: 4 additions & 0 deletions NAMESPACE
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# Generated by roxygen2: do not edit by hand

export(exportCellRanger)
export(exportIgBLAST)
export(exportMiXCR)
export(exportTRUST4)
export(getIMGT)
export(getOGRDB)
export(is_imgt_available)
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21 changes: 21 additions & 0 deletions NEWS.md
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# immReferent VERSION 1.0.1

## New Features

* 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

## Documentation Improvements

* 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
* Enhanced package-level documentation with function overview
* Fixed typo in `is_ogrdb_available()` documentation (was incorrectly
referencing IMGT)

# immReferent VERSION 0.99.5

* Added package level man page
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