immLynx
Bioc currentLinking Advanced TCR Python Pipelines and Hugging Face Models in R
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
A comprehensive toolkit that bridges popular Python-based immune repertoire analysis tools and Hugging Face protein language models into the R environment. Provides unified interfaces for TCR distance calculations (tcrdist3), sequence generation probability (OLGA), selection inference (soNNia), clustering (clusTCR), protein embeddings (ESM-2), metaclone discovery (metaclonotypist). Fully compatible with the scRepertoire and immApex ecosystem for single-cell immune repertoire analysis.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
22 15 exported
Complexity
8.8 avg / 40 max
Call network
22 nodes / 14 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
11,835
Files
103
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
15
Internal functions
7
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
2.53
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
22.2%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 4%
Topics
People
- Nick Borcherding author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
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