igblastr
This is the released version of igblastr; for the devel version, see igblastr.
User-friendly R Wrapper to IgBLAST
Bioconductor version: Release (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, annotations for the V and J alleles in a new germline database are automatically computed and added to the database, so they can be used as replacements for the internal and auxiliary 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")
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 | ||
| NEWS | Text |
Details
| biocViews | CellBiology, ImmunoOncology, Immunogenetics, Immunology, Software |
| Version | 1.2.5 |
| In Bioconductor since | BioC 3.22 (R-4.5) (0.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0), tibble, Biostrings |
| Imports | methods, utils, stats, tools, R.utils, curl, httr, xml2, rvest, xtable, jsonlite, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb |
| 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_1.2.5.tar.gz |
| Windows Binary (x86_64) | igblastr_1.2.3.zip |
| macOS Binary (big-sur-x86_64) | igblastr_1.2.3.tgz |
| macOS Binary (sonoma-arm64) | igblastr_1.2.3.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 |
| Old Source Packages for BioC 3.23 | Source Archive |