immReferent
This is the released version of immReferent; for the devel version, see immReferent.
An Interface for Immune Receptor and HLA Gene Reference Data
Bioconductor version: Release (3.23)
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.
Author: Nick Borcherding [aut, cre]
Maintainer: Nick Borcherding <ncborch at gmail.com>
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.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("immReferent")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("immReferent")| Caching and Offline Usage of Reference Sets (IMGT & OGRDB) | HTML | R Script |
| Getting Started with immReferent | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | Biostrings, httr, jsonlite, methods, rvest, tibble, yaml |
| System Requirements | |
| URL | https://github.com/BorchLab/immReferent/ |
| Bug Reports | https://github.com/BorchLab/immReferent/issues |
See More
| Suggests | BiocManager, BiocStyle, knitr, mockery, spelling, rmarkdown, testthat (>= 3.0.0), withr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | immApex |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow 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 (big-sur-x86_64) | immReferent_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | immReferent_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/immReferent |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/immReferent |
| Package Short Url | https://bioconductor.org/packages/immReferent/ |
| Package Downloads Report | Download Stats |