SamSPECTRAL
Bioc currentIdentifies cell population in flow cytometry data
Release Lineage
Entered 2.6 · Apr 23, 2010
Current · Requires R 4.6
Description
Samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting "connected components" estimate biological cell populations in the data. See the vignette for more details on how to use this package, some illustrations, and simple examples.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
14 0 exported
Complexity
14.3 avg / 30 max
Call network
14 nodes / 13 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
2,702
Files
30
Compiled share
11.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
7
Internal functions
0
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.3.3
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
33
First release
2010-05-04
Latest release
2026-04-28
Avg cadence
182 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
- 12includes a package overview page
- Examples that run
- 42%5 run in a plain check · 7 never run
- Exported functions with examples
- 100%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 100%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| eigen.values.10 | vector | 1,553 elements | No other package |
| eigen.values.1000 | vector | 1,536 elements | No other package |
| small | matrix | 9,000 × 3 | No other package |
| stmFSC | – | – | – |
Topics
Depended on by (2)
Bioconductor (2)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SamSPECTRAL")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.