betterChromVAR
Bioc currentImproved ChromVAR (Chromatin Variation Across Regions)
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
A much faster analytical implementation of chromVAR, with additional features, used to infer TF activity from (bulk or single-cell) ATAC-seq data and motif annotations (or binding probabilities). The package also includes the CVnorm normalization method based on the chromVAR logic.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
17 11 exported
Complexity
8.1 avg / 25 max
Call network
17 nodes / 22 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
2,193
Files
28
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
6
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
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-05-07
Latest release
2026-05-07
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
- 13
- Examples that run
- 91%10 run in a plain check · 1 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 23% with a bibliography file
Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/plger/betterchromvar on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Topics
People
- Pierre-Luc Germain author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("betterChromVAR")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 v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.