chromVAR
Bioc currentChromatin Variation Across Regions
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
133 22 exported
Complexity
3.1 avg / 15 max
Call network
133 nodes / 103 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
8,146
Files
100
Compiled share
4.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
37
Internal functions
92
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
–
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
3.4
System requirements
1 externalC++14
C++ standard
C++14
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
18
First release
2018-04-02
Latest release
2026-05-07
Avg cadence
182 days
Cold removal rate
–
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 48includes a package overview page
- Examples that run
- 100%39 run in a plain check
- Exported functions with examples
- 84%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Introduction HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
2 practices detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| counts_table | data.frame | 11 × 17 | No other package |
| example_counts | – | – | – |
| mini_counts | – | – | – |
| mini_dev | – | – | – |
| mini_ix | – | – | – |
| test_bed | data.frame | 10 × 5 | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People
- Alicia Schep author maintainer
- Stanford University copyright holder
- Jason Buenrostro contributor
- William Greenleaf thesis advisor
- Caleb Lareau contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("chromVAR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/nmeth.4401.
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.