BulkSignalR
Bioc currentInfer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
Inference of ligand-receptor (LR) interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics. BulkSignalR bases its inferences on the LRdb database included in our other package, SingleCellSignalR available from Bioconductor. It relies on a statistical model that is specific to bulk data sets. Different visualization and data summary functions are proposed to help navigating prediction results.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
79 41 exported
Complexity
6.7 avg / 26 max
Call network
79 nodes / 41 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
18,610
Files
203
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
40
Internal functions
38
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
6.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5
System requirements
–
C++ standard
–
License
CeCILL | file LICENSE
License flags
not SPDX, not OSI
History
Versions
3
First release
2025-09-27
Latest release
2026-04-28
Avg cadence
107 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 155 (51 internal)includes a package overview page
- Examples that run
- 100%85 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/jcolinge/bulksignalr on 2026-10-22.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| annotation.spa | – | – | – |
| bodyMap.mouse | data.frame | 24,543 × 8 | No other package |
| bsrdm | – | – | – |
| bsrdm.comp | – | – | – |
| bsrdm.spa | – | – | – |
| bsrinf | – | – | – |
| bsrinf.comp | – | – | – |
| bsrinf.mouse | – | – | – |
| bsrinf.spa | – | – | – |
| immune.signatures | data.frame | 1,541 × 2 | No other package |
| ortholog.dict | data.frame | 4,572 × 1 | No other package |
| p.EMT | data.frame | 100 × 1 | No other package |
| sdc | data.frame | 19,764 × 26 | No other package |
| tme.signatures | data.frame | 213 × 2 | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People
- Jean-Philippe Villemin maintainer
- Jacques Colinge author
Cite
Cite this package
Run in R for the authors' entry:
citation("BulkSignalR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/nar/gkad352.
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.