xCell2
Bioc currentA Tool for Generic Cell Type Enrichment Analysis
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
xCell2 provides methods for cell type enrichment analysis using cell type signatures. It includes three main functions - 1. xCell2Train for training custom references objects from bulk or single-cell RNA-seq datasets. 2. xCell2Analysis for conducting the cell type enrichment analysis using the custom reference. 3. xCell2GetLineage for identifying dependencies between different cell types using ontology.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
12 3 exported
Complexity
7.1 avg / 18 max
Call network
12 nodes / 11 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
4,040
Files
50
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
13
Internal functions
9
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.16
testthat edition
–
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
4.0.0
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2025-10-06
Latest release
2026-04-28
Avg cadence
102 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 21
- Examples that run
- 100%8 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 5%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/almogangel/xcell2 on 2026-10-11.
GitHub Pages site last deployed 2025-12-11
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| BlueprintEncode.xCell2Ref | – | – | – |
| DICE_demo.xCell2Ref | – | – | – |
| ImmGenData.xCell2Ref | – | – | – |
| ImmuneCompendium.xCell2Ref | – | – | – |
| LM22.xCell2Ref | – | – | – |
| MouseRNAseqData.xCell2Ref | – | – | – |
| PanCancer.xCell2Ref | – | – | – |
| TMECompendium.xCell2Ref | – | – | – |
| TabulaMurisBlood.xCell2Ref | – | – | – |
| TabulaSapiensBlood.xCell2Ref | – | – | – |
| dice_demo_ref | – | – | – |
| mix_demo | matrix | 1,000 × 3 | No other package |
Topics
Suggested by (1)
People
- Almog Angel author maintainer
- Dvir Aran author
Cite
Cite this package
Run in R for the authors' entry:
citation("xCell2")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1101/2024.09.06.611424.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.