StabMap
Bioc currentStabilised mosaic single cell data integration using unshared features
Release Lineage
Entered 3.20 · Oct 30, 2024
Current · Requires R 4.6
Description
StabMap performs single cell mosaic data integration by first building a mosaic data topology, and for each reference dataset, traverses the topology to project and predict data onto a common embedding. Mosaic data should be provided in a list format, with all relevant features included in the data matrices within each list object. The output of stabMap is a joint low-dimensional embedding taking into account all available relevant features. Expression imputation can also be performed using the StabMap embedding and any of the original data matrices for given reference and query cell lists.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
30 9 exported
Complexity
4.1 avg / 44 max
Call network
30 nodes / 23 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
15,395
Files
129
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
9
Internal functions
17
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
6.51
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
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
4
First release
2024-10-29
Latest release
2026-04-28
Avg cadence
168 days
Cold removal rate
–
Dep drift
0
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
- 96%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Shila Ghazanfar author maintainer contributor
- Aiden Jin contributor
- Nicholas Robertson contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("StabMap")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 v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.