Package: immReferent 1.1.0

Nick Borcherding

immReferent: An Interface for Immune Receptor and HLA Gene Reference Data

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.

Authors:Nick Borcherding [aut, cre]

immReferent_1.1.0.tar.gz
immReferent_1.1.0.zip(r-4.7)immReferent_1.1.0.zip(r-4.6)immReferent_1.1.0.zip(r-4.5)
immReferent_1.1.0.tgz(r-4.6-any)immReferent_1.1.0.tgz(r-4.5-any)
immReferent_1.1.0.tar.gz(r-4.7-any)immReferent_1.1.0.tar.gz(r-4.6-any)
immReferent_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
immReferent/json (API)

# Install 'immReferent' in R:
install.packages('immReferent', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/borchlab/immreferent/issues

On BioConductor:immReferent-1.1.0(bioc 3.24)immReferent-1.0.0(bioc 3.23)

softwareannotationsequencing

7.08 score 9 stars 5 packages 6 scripts 172 downloads 14 exports 30 dependencies

Last updated from:ec8d075a73. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING189
linux-devel-x86_64OK310
source / vignettesOK261
linux-release-x86_64OK286
macos-release-arm64OK147
macos-oldrel-arm64OK210
windows-develOK233
windows-releaseOK227
windows-oldrelOK234
wasm-releaseOK145

Exports:exportCellRangerexportIgBLASTexportMiXCRexportTRUST4getIMGTgetOGRDBis_imgt_availableis_ogrdb_availablelistIMGTlistOGRDBloadIMGTloadOGRDBrefreshIMGTrefreshOGRDB

Dependencies:askpassBiocGenericsBiostringsclicrayoncurlgenericsgluehttrIRangesjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigR6rlangrvestS4VectorsselectrSeqinfosystibbleutf8vctrsxml2XVectoryaml

Getting Started with immReferent
Introduction | Installation | Downloading Reference Sequences | Downloading HLA Sequences (IPD-IMGT/HLA) | Downloading TCR/BCR Sequences (IMGT) | Downloading Germline Sets from OGRDB (AIRR) | Working with the Cache | Listing Cached Files | Loading from Cache | Refreshing the Cache | Exporting Reference Databases for External Tools | Export to MiXCR | Export to TRUST4 | Export to Cell Ranger VDJ | Export to IgBLAST | Conclusion | Session Info
Rendered fromimmReferent.Rmdusingknitr::rmarkdown

Last update: 2026-04-03
Started: 2025-10-14

Caching and Offline Usage of Reference Sets (IMGT & OGRDB)
Introduction | The Cache Directory | Finding the Cache | Changing the Cache Location | Offline Workflow | Cache Metadata
Rendered fromcaching.Rmdusingknitr::rmarkdown

Last update: 2025-09-08
Started: 2025-08-20