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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/immReferent/ |
| Package Short Url | https://bioconductor.org/packages/immReferent/ |
| Package Downloads Report | Download Stats |