celda
Bioc currentCEllular Latent Dirichlet Allocation
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
Celda is a suite of Bayesian hierarchical models for clustering single-cell RNA-sequencing (scRNA-seq) data. It is able to perform "bi-clustering" and simultaneously cluster genes into gene modules and cells into cell subpopulations. It also contains DecontX, a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. A variety of scRNA-seq data visualization functions is also included.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
284 20 exported
Complexity
4 avg / 44 max
Call network
284 nodes / 371 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
33,532
Files
394
Compiled share
5.1%
Has compiled src
Yes
Language breakdown
API
Exported functions
71
Internal functions
216
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
33
Dep constraint coverage
2.6%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-06-03
Latest release
2026-04-28
Avg cadence
190 days
Cold removal rate
100%
Dep drift
31
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 99%
- Documented parameters
- 99%
- Return-value docs
- 98%
- References docs
- 0%
Topics
Depended on by (2)
Bioconductor (2)
People
- Joshua Campbell author maintainer
- Sean Corbett author
- Yusuke Koga author
- Zhe Wang author
- Shiyi Yang author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("celda")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.