EasyCellType
Bioc currentAnnotate cell types for scRNA-seq data
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA) and a modified versio of Fisher's exact test. The function presents annotation recommendations in graphical outcomes: bar plots for each cluster showing candidate cell types, as well as a dot plot summarizing the top 5 significant annotations for each cluster.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
8 5 exported
Complexity
3.6 avg / 8 max
Call network
8 nodes / 5 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
1,180
Files
43
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
3
Testing
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
8.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-11-01
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 13
- Examples that run
- 80%4 run in a plain check · 1 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- my-vignette HTML
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 |
|---|---|---|---|
| cellmarker_tissue | list | 2 elements | No other package |
| clustermole_tissue | list | 2 elements | No other package |
| gene_pbmc | data.frame | 2,701 × 3 | No other package |
| panglao_tissue | list | 2 elements | No other package |
| pbmc_data | dgCMatrix | 32,738 × 2,700 | No other package |
3 internal objects are bundled for the package's own use and not listed here.
Topics
People
- Ruoxing Li author maintainer contributor
- Ziyi Li contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("EasyCellType")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 v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.