esATAC
Bioc currentAn Easy-to-use Systematic pipeline for ATACseq data analysis
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
165 34 exported
Complexity
2.1 avg / 16 max
Call network
165 nodes / 64 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
14,962
Files
134
Compiled share
17.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
34
Internal functions
52
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
2.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0.0
System requirements
1 externalC++11
C++ standard
–
License
GPL-3 | file LICENSE
License flags
SPDX valid, not OSI
History
Versions
18
First release
2018-03-07
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
10
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 34includes a package overview page
- Examples that run
- 78%25 run in a plain check · 7 never run
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 6%
Repository practices
Checks run against github.com/wzthu/esatac on 2026-10-22.
No development-tooling practices detected in the upstream repository.
Datasets
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("esATAC")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/bty141.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.