scMerge
Bioc currentscMerge: Merging multiple batches of scRNA-seq data
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
Like all gene expression data, single-cell data suffers from batch effects and other unwanted variations that makes accurate biological interpretations difficult. The scMerge method leverages factor analysis, stably expressed genes (SEGs) and (pseudo-) replicates to remove unwanted variations and merge multiple single-cell data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of single-cell data.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
49 11 exported
Complexity
5.9 avg / 24 max
Call network
49 nodes / 50 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
6,589
Files
57
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
38
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.29
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
15.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-05-02
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
23
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 14
- Examples that run
- 100%11 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 97%
- Return-value docs
- 91%
- Help pages citing references
- 14%
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/sydneybiox/scmerge on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows
GitHub Pages site last deployed 2024-04-12 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| example_sce | – | – | – |
| segList | list | 2 elements | No other package |
| segList_ensemblGeneID | list | 2 elements | No other package |
Topics
Depended on by (2)
Bioconductor (2)
Suggested by (1)
People
- Yingxin Lin author maintainer
- Sydney Bioinformatics and Biometrics Group funder
- Kevin Wang author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("scMerge")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.