. IgBLAST web interface:
. OGRDB:
. IMGT/V-QUEST download site:
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Bioconductor - igblastr
Bioconductor 3.22
Software Packages
igblastr
igblastr
This is the
released
version of igblastr; for the devel version, see
igblastr
User-friendly R Wrapper to IgBLAST
DOI:
10.18129/B9.bioc.igblastr
Bioconductor version:
Release (3.22)
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
. IgBLAST web interface:
. OGRDB:
. IMGT/V-QUEST download site:
Author:
Hervé Pagès [aut, cre]
ORCID: 0009-0002-8272-4522
, Ollivier Hyrien [aut, fnd]
ORCID: 0000-0003-1909-2542
, Kellie MacPhee [ctb]
ORCID: 0009-0008-0993-4009
, Michael Duff [ctb]
ORCID: 0009-0008-4279-0756
, Jason Taylor [ctb]
Maintainer:
Hervé Pagès
Citation (from within R, enter
citation("igblastr")
):
Installation
To install this package, start R (version "4.5") 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
PDF
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
CellBiology
ImmunoOncology
Immunogenetics
Immunology
Software
Version
1.0.23
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
(>= 1.46.2)
System Requirements
URL
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See More
Suggests
GenomicAlignments
, parallel,
testthat
knitr
rmarkdown
BiocStyle
ggplot2
dplyr
scales
ggseqlogo
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Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
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Build Report
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Installation
instructions to use this package in your R session.
Source Package
igblastr_1.0.23.tar.gz
Windows Binary (x86_64)
igblastr_1.0.23.zip
macOS Binary (x86_64)
igblastr_1.0.23.tgz
macOS Binary (arm64)
igblastr_1.0.23.tgz
Source Repository
git clone https://git.bioconductor.org/packages/igblastr
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/igblastr
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