extraChIPs
Bioc currentAdditional functions for working with ChIP-Seq data
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
105 16 exported
Complexity
5.2 avg / 33 max
Call network
105 nodes / 60 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
21,548
Files
193
Compiled share
16.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
39
Internal functions
79
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.30
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
3
Dep constraint coverage
16.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-08-31
Latest release
2026-06-29
Avg cadence
156 days
Cold removal rate
–
Dep drift
17
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 46 (5 internal)includes a package overview page
- Examples that run
- 93%38 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 100%
- Documented parameters
- 79%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/smped/extrachips on 2026-10-18.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| ex_genes | – | – | – |
| ex_hic | – | – | – |
| ex_prom | – | – | – |
| ex_trans | – | – | – |
| grch37.cytobands | data.frame | 862 × 5 | No other package |
| grch38.cytobands | data.frame | 862 × 5 | No other package |
| peaks | – | – | – |
| se | – | – | – |
Topics
Suggested by (2)
People
- Stevie Pederson author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("extraChIPs")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 v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.