Ibex
Bioc currentMethods for BCR single-cell embedding
Release Lineage
Entered 3.22 · Oct 30, 2025
Current · Requires R 4.6
Description
Implementation of the Ibex algorithm for single-cell embedding based on BCR sequences. The package includes a standalone function to encode BCR sequence information by amino acid properties or sequence order using tensorflow-based autoencoder. In addition, the package interacts with SingleCellExperiment or Seurat data objects.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
19 4 exported
Complexity
4.4 avg / 15 max
Call network
19 nodes / 17 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
2,198
Files
69
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
4
Internal functions
14
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.39
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
16.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
1
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2025-10-29
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 97%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Nick Borcherding author maintainer cph
- Qile Yang contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("Ibex")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.