BatChef
Bioc currentSingle-cell RNA-seq batch effects correction methods interface
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
This package implements a variety of methods for batch correction in single-cell RNA sequencing (scRNA-seq) data. It incorporates quantitative metrics (e.g. Wasserstein distance, Adjusted Rand Index) to evaluate their performance. Furthermore, the package assists users in identifying and applying the optimal method for specific datasets.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
44 26 exported
Complexity
1.5 avg / 5 max
Call network
44 nodes / 29 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
5,423
Files
104
Compiled share
2.3%
Has compiled src
Yes
Language breakdown
API
Exported functions
27
Internal functions
14
Recent export changes
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
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-06-26
Latest release
2026-06-26
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 47 (1 internal)includes a package overview page
- Examples that run
- 100%19 run in a plain check
- Exported functions with examples
- 95%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- BatChef vignette HTML
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/zuinelena3/batchef on 2026-10-18.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| res | list | 4 elements | No other package |
Topics
People
-
Elena Zuin
author
maintainer
Department of Biology, University of Padova
-
Davide Risso
contributor
Department of Statistical Sciences, University of Padova
-
Chiara Romualdi
contributor
Department of Biology, University of Padova
-
Gabriele Sales
contributor
Department of Biology, University of Padova
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("BatChef")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 v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.