atacInferCnv
Bioc currentCall CNV from single cell ATAC-seq data based on InferCNV adaptation
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
The package prepares input scATAC-seq data and adapts for copy number variance profiling with InferCNV package usage. It has also various paramters to control the analysis (e.g. external normal reference usage, meta-cells, bin size, etc) and custom plot visualizations.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
16 3 exported
Complexity
5.8 avg / 22 max
Call network
16 nodes / 12 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
1,515
Files
29
Compiled share
5%
Has compiled src
Yes
Language breakdown
API
Exported functions
3
Internal functions
9
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.14
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
16.7%
Unsafe pattern score
0
Dep constraint coverage
7.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.6.0
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
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
- 7includes a package overview page
- Examples that run
- 100%3 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/kokonech/atacinfercnv on 2026-10-22.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| MB183_ATAC_subset | data.frame | 80,716 × 300 | No other package |
| MB183_ATAC_subset.CNV_blocks_ann | data.frame | 300 × 2 | No other package |
| MB183_ATAC_subset.CNV_blocks_ann_n30 | data.frame | 30 × 2 | No other package |
Topics
People
- Konstantin Okonechnikov author maintainer
- Supat Thongjuea author funder
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("atacInferCnv")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.