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.
None published for Bioconductor
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
61
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
9
Internal functions
17
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
6.51
testthat edition
3
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
- Help pages
- 29 (20 internal)
- Examples that run
- 100%9 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 96%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
4 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/sydneybiox/stabmap on 2026-10-18.
GitHub Pages site last deployed 2024-10-15 · The repository has a site deploy workflow
pkgdown site last built 2024-10-15
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 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.