celldex
Bioc currentIndex of Reference Cell Type Datasets
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
25 15 exported
Complexity
3.4 avg / 11 max
Call network
25 nodes / 35 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
2,510
Files
52
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
16
Internal functions
10
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.13
testthat edition
–
Docs
Roxygen coverage
100%
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
–
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2020-10-27
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 13 (1 internal)
- Examples that run
- 100%12 run in a plain check
- Exported functions with examples
- 92%
- Documented parameters
- 88%
- Return-value docs
- 92%
- Help pages citing references
- 54%
- Cell type references HTML
Repository practices
2 development-tooling and community-health practices detected across 1 family in the upstream repository
Checks run against github.com/ltla/celldex on 2026-10-21.
The R CMD check workflow runs on Linux, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| metadata-blueprint_encode | data.frame | 2 × 15 | No other package |
| metadata-dice | data.frame | 2 × 15 | No other package |
| metadata-dmap | data.frame | 2 × 15 | No other package |
| metadata-hpca | data.frame | 2 × 15 | No other package |
| metadata-immgen | data.frame | 2 × 15 | No other package |
| metadata-monaco_immune | data.frame | 2 × 15 | No other package |
| metadata-mouse.rnaseq | data.frame | 2 × 15 | No other package |
Topics
Depended on by (4)
Show all 13 packagesHide all 13 packages
Bioconductor (4)
Suggested by (9)
People
- Aaron Lun author maintainer copyright holder
- Jared Andrews author
- Dvir Aran author
- Daniel Bunis author
- Friederike Dündar author
Cite
Cite this package
Run in R for the authors' entry:
citation("celldex")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/s41590-018-0276-y.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.