immReferent
This is the development version of immReferent; to use it, please install the devel version of Bioconductor.
An Interface for Immune Receptor and HLA Gene IMGT Reference Data
Bioconductor version: Development (3.23)
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.
Author: Nick Borcherding [aut, cre]
Maintainer: Nick Borcherding <ncborch at gmail.com>
citation("immReferent")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | Annotation, Sequencing, Software |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| 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 | |
| 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_0.99.5.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | immReferent_0.99.5.tgz |
| macOS Binary (arm64) | immReferent_0.99.5.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 |