igblastr
This is the development version of igblastr; for the stable release version, see igblastr.
User-friendly R Wrapper to IgBLAST
Bioconductor version: Development (3.23)
The igblastr package provides functions to conveniently install and use a local IgBLAST installation from within R. The package also includes a set of built-in IgBLAST-compatible germline databases from OGRDB, the AIRR Community’s Open Germline Receptor Database, for various organisms. It provides functions to create additional IgBLAST-compatible germline databases using reference sequences retrieved from IMGT/V-QUEST or local FASTA files supplied by the user. When possible, the FWR/CDR boundaries on the V alleles (a.k.a "internal data") are computed and stored in the germline database, so can be used as a replacement for the internal data shipped with IgBLAST. IgBLAST is described at
Author: Hervé Pagès [aut, cre]
, Ollivier Hyrien [aut, fnd]
, Kellie MacPhee [ctb]
, Michael Duff [ctb]
, Jason Taylor [ctb]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("igblastr")):
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("igblastr")
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("igblastr")| igblastr overview | HTML | R Script |
| Reference Manual |
Details
| biocViews | CellBiology, ImmunoOncology, Immunogenetics, Immunology, Software |
| Version | 1.1.18 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0), tibble, Biostrings |
| Imports | methods, utils, stats, tools, R.utils, curl, httr, xml2, rvest, xtable, jsonlite, S4Vectors, IRanges, GenomeInfoDb(>= 1.47.2) |
| System Requirements | |
| URL | https://bioconductor.org/packages/igblastr |
| Bug Reports | https://github.com/HyrienLab/igblastr/issues |
See More
| Suggests | GenomicAlignments, parallel, testthat, knitr, rmarkdown, BiocStyle, ggplot2, dplyr, scales, ggseqlogo |
| 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 | igblastr_1.1.18.tar.gz |
| Windows Binary (x86_64) | igblastr_1.1.13.zip |
| macOS Binary (big-sur-x86_64) | igblastr_1.1.11.tgz |
| macOS Binary (big-sur-arm64) | igblastr_1.1.11.tgz |
| macOS Binary (sonoma-arm64) | igblastr_1.1.13.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/igblastr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/igblastr |
| Bioc Package Browser | https://code.bioconductor.org/browse/igblastr/ |
| Package Short Url | https://bioconductor.org/packages/igblastr/ |
| Package Downloads Report | Download Stats |