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.
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
197
Compiled share
16.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
39
Internal functions
79
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.30
testthat edition
3
CI present
No
CI type
[]
PR gated
No
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
- Examples that run
- 93%
- Documented parameters
- 79%
- Return-value docs
- 100%
- References docs
- 0%
Topics
Depended on by (2)
Bioconductor (2)
People
- Stevie Pederson author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("extraChIPs")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.