immReferent
An Interface for Immune Receptor and HLA Gene Reference Data
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("immReferent")Details
| Maintainer | Nick Borcherding <ncborch@gmail.com> |
| Author | Nick Borcherding [aut, cre] |
| License | MIT + file LICENSE |
| URL | https://github.com/BorchLab/immReferent/ |
| Bug Reports | https://github.com/BorchLab/immReferent/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/immReferent/ |
Citation
From within R, enter citation("immReferent"):
Nick Borcherding. immReferent: An Interface for Immune Receptor and HLA Gene Reference Data. doi:10.18129/B9.bioc.immReferent, R package version 1.0.0, https://bioconductor.org/packages/immReferent.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | immReferent_1.0.0.tar.gz |
| Windows binary (x86_64) | immReferent_1.0.0.zip |
| macOS binary (arm64) | immReferent_1.0.0.tgz |
| macOS binary (x86_64) | immReferent_1.0.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: Biostrings, httr, jsonlite, methods, rvest, tibble, yaml
Suggests: BiocManager, BiocStyle, knitr, mockery, spelling, rmarkdown, testthat (>= 3.0.0), withr
Reverse dependencies
Imports Me (1): immApex