COMPASS
Bioc currentCombinatorial Polyfunctionality Analysis of Single Cells
Release Lineage
Entered 2.14 · Apr 14, 2014
Current · Requires R 4.6
Description
COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
133 35 exported
Complexity
4.8 avg / 47 max
Call network
133 nodes / 99 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
10,810
Files
154
Compiled share
23%
Has compiled src
Yes
Language breakdown
API
Exported functions
35
Internal functions
70
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.08
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
50%
Unsafe pattern score
14
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.0.3
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
25
First release
2014-05-09
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
11
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 41includes a package overview page
- Examples that run
- 93%27 run in a plain check (1 of them under a condition) · 2 never run
- Exported functions with examples
- 76%
- Documented parameters
- 98%
- Return-value docs
- 41%
- Help pages citing references
- 0%
- SimpleCOMPASS PDF
- COMPASS HTML
Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/rglab/compass on 2026-10-18.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| CC | COMPASSContainer | 5 elements | No other package |
| CR | COMPASSResult | 3 elements | No other package |
| SimpleCOMPASSExamples | data.frame | 42 × 261 | No other package |
Topics
People
- Greg Finak author maintainer
-
Raivo Kolde
contributor
Author of 'pheatmap', which was modified and now used internally in COMPASS
- Lynn Lin author
- Kevin Ushey author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("COMPASS")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.