DiffBind
Bioc currentDifferential Binding Analysis of ChIP-Seq Peak Data
Release Lineage
Entered 2.9 · Nov 1, 2011
Current · Requires R 4.6
Description
Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
437 20 exported
Complexity
9.9 avg / 120 max
Call network
437 nodes / 564 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
26,722
Files
131
Compiled share
9.7%
Has compiled src
Yes
Language breakdown
API
Exported functions
114
Internal functions
260
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.04
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
3
Dep constraint coverage
3.4%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
1 externalGNU make
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
30
First release
2012-03-18
Latest release
2026-07-01
Avg cadence
183 days
Cold removal rate
100%
Dep drift
28
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 25includes a package overview page
- Examples that run
- 95%21 run in a plain check · 1 never run
- Exported functions with examples
- 95%
- Documented parameters
- 97%
- Return-value docs
- 100%
- Help pages citing references
- 84%
- Fix bug where
bSubControlset indba.count()was not preserved on the returned object, so a subsequentdba.normalize()(and hencedba.analyze()) could silently fall back to control subtraction based onis.null(greylist)rather than honoring the value used for counting.pv.counts()now re-stampsbSubControlonto the reconstructed object and forwards it through the summit re-centering step. Reported by Tomasz Wlodarczyk and Xiaosai Yao.
From inst/NEWS.Rd in the release
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| tamoxifen | DBA | 25 elements | No other package |
| tamoxifen.greylist | list | 2 elements | No other package |
Topics
Depended on by (2)
Suggested by (1)
People
- Rory Stark author maintainer
- Gord Brown author
Cite
Cite this package
Run in R for the authors' entry:
citation("DiffBind")The package provides a citation file, so citation() returns the authors' own entry.
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.