ATACseqTFEA
Bioc currentTranscription Factor Enrichment Analysis for ATAC-seq
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
Assay for Transpose-Accessible Chromatin using sequencing (ATAC-seq) is a technique to assess genome-wide chromatin accessibility by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. ATACseqTFEA is an improvement of the current computational method that detects differential activity of transcription factors (TFs). ATACseqTFEA not only uses the difference of open region information, but also (or emphasizes) the difference of TFs footprints (cutting sites or insertion sites). ATACseqTFEA provides an easy, rigorous way to broadly assess TF activity changes between two conditions.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
22 15 exported
Complexity
3.5 avg / 11 max
Call network
22 nodes / 17 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
3,100
Files
67
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
18
Internal functions
7
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
–
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
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-11-04
Latest release
2026-04-28
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
- Examples that run
- 100%
- Documented parameters
- 82%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Jianhong Ou author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ATACseqTFEA")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.