batchelor
Bioc currentSingle-Cell Batch Correction Methods
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression values. Functions are also provided to perform global rescaling to remove differences in depth between batches, and to perform a principal components analysis that is robust to differences in the numbers of cells across batches.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
114 27 exported
Complexity
4.1 avg / 16 max
Call network
114 nodes / 167 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
12,358
Files
89
Compiled share
3.3%
Has compiled src
Yes
Language breakdown
API
Exported functions
29
Internal functions
78
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.83
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
1 externalC++11
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-05-22
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
8
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 23 (1 internal)
- Examples that run
- 100%22 run in a plain check
- Exported functions with examples
- 95%
- Documented parameters
- 99%
- Return-value docs
- 95%
- Help pages citing references
- 17%
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.
Topics
Depended on by (12)
Show all 16 packagesHide all 16 packages
Bioconductor (12)
Suggested by (4)
People
- Aaron Lun author maintainer
- Laleh Haghverdi contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("batchelor")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/nbt.4091.
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.