igblastr
Bioc currentUser-friendly R Wrapper to IgBLAST
Release Lineage
Entered 3.22 · Oct 30, 2025
Current · Requires R 4.6
Description
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 <https://pubmed.ncbi.nlm.nih.gov/23671333/>. IgBLAST web interface: <https://www.ncbi.nlm.nih.gov/igblast/>. OGRDB: <https://ogrdb.airr-community.org/>. IMGT/V-QUEST download site: <https://www.imgt.org/download/V-QUEST/>.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
693 121 exported
Complexity
2.8 avg / 17 max
Call network
693 nodes / 1304 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
26,017
Files
599
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
125
Internal functions
526
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.16
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
37.5%
Unsafe pattern score
2
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2026-03-16
Latest release
2026-09-17
Avg cadence
185 days
Cold removal rate
100%
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 45
- Examples that run
- 88%38 run in a plain check · 3 never run · 2 hold no code
- Exported functions with examples
- 98%
- Documented parameters
- 95%
- Return-value docs
- 98%
- Help pages citing references
- 2%
- igblastr overview HTML
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/hyrienlab/igblastr on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
Topics
People
- Hervé Pagès author maintainer
- Michael Duff contributor
- Ollivier Hyrien author funder
- Kellie MacPhee contributor
- Jason Taylor contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("igblastr")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.18129/b9.bioc.igblastr.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.