SingleCellAlleleExperiment
Bioc currentS4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
Defines a S4 class that is based on SingleCellExperiment. In addition to the usual gene layer the object can also store data for immune genes such as HLAs, Igs and KIRs at allele and functional level. The package is part of a workflow named single-cell ImmunoGenomic Diversity (scIGD), that firstly incorporates allele-aware quantification data for immune genes. This new data can then be used with the here implemented data structure and functionalities for further data handling and data analysis.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
18 3 exported
Complexity
3.1 avg / 9 max
Call network
18 nodes / 22 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
2,606
Files
38
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
3
Internal functions
15
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.31
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
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-04-30
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
- 19
- Examples that run
- 100%3 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/agimkeller/singlecellalleleexperiment on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Topics
Suggested by (1)
People
- Jonas Schuck author maintainer
- Ahmad Al Ajami author
- Katharina Imkeller author
- Federico Marini author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SingleCellAlleleExperiment")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 v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.