igblastr
This is the development version of igblastr; for the stable release version, see igblastr.
User-friendly R Wrapper to IgBLAST
Bioconductor version: Development (3.24)
The igblastr package provides functions to conveniently install and use a local IgBLAST installation from within R. The package also includes a set of preinstalled IgBLAST-compatible germline databases from OGRDB, the AIRR Community’s Open Germline Receptor Database, for various organisms. It provides functions to install additional IgBLAST-compatible germline databases using reference sequences retrieved from IMGT/V-QUEST or OGRDB, or from local FASTA files supplied by the user. When possible, annotations for the V and J alleles in a new germline database are automatically generated and added to the database, so they can be used as replacements for the internal and auxiliary data provided by 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")):
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")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | CellBiology, ImmunoOncology, Immunogenetics, Immunology, Software |
| Version | 1.3.19 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| 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 | Peptides, GenomicAlignments, parallel, testthat, knitr, rmarkdown, BiocStyle, ggplot2, dplyr, scales, ggseqlogo, airr |
| 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_1.3.19.tar.gz |
| Windows Binary (x86_64) | igblastr_1.3.17.zip |
| macOS Binary (big-sur-x86_64) | igblastr_1.3.19.tgz |
| macOS Binary (sonoma-arm64) | igblastr_1.3.19.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 |