ATACseqQC
Bioc currentATAC-seq Quality Control
Release Lineage
Entered 3.5 · Apr 25, 2017
Current · Requires R 4.6
Description
ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
49 23 exported
Complexity
7.5 avg / 36 max
Call network
49 nodes / 42 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
6,697
Files
93
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
23
Internal functions
26
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.04
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
83.3%
Unsafe pattern score
0
Dep constraint coverage
4.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.4
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
19
First release
2017-08-28
Latest release
2026-07-13
Avg cadence
186 days
Cold removal rate
–
Dep drift
9
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
- 78%
- Return-value docs
- 100%
- References docs
- 19%
Topics
Depended on by (4)
Bioconductor (4)
People
Jianhong Ou
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ATACseqQC")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.