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quaqcr  

Quick ATAC-Seq QC
View on CRAN: Click here


Download and install quaqcr package within the R console
Install from CRAN:
install.packages("quaqcr")

Install from Github:
library("remotes")
install_github("cran/quaqcr")

Install by package version:
library("remotes")
install_version("quaqcr", "1.0.4")



Attach the package and use:
library("quaqcr")
Maintained by
Benjamin Jean-Marie Tremblay
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-05-19
Latest Update: 2026-05-19
Description:
A wrapper around the 'quaqc' program described in Tremblay and Questa (2024) <doi:10.1093/bioinformatics/btae649>. 'quaqc' allows for assay for transposase-accessible chromatin using sequencing (ATAC-seq) specific quality control and read filtering of next-generation sequencing (NGS) data with minimal processing time and extremely low memory overhead. Any number of samples can be processed, using multiple threads if desired. 'quaqc' outputs a comprehensive set of aligned read metrics, including alignment size, fragment size, percent duplicates, mapq scores, read depth, GC content, and others. Although designed for ATAC-seq data, 'quaqc' can also be used for other unspliced DNA sequencing experiments (such as chromatin immunoprecipitation sequencing, or ChIP-seq) as many of the metrics are related to general sequencing quality. This R package also provides additional utilities for custom analyses and plotting of 'quaqc' results.
How to cite:
Benjamin Jean-Marie Tremblay (2026). quaqcr: Quick ATAC-Seq QC. R package version 1.0.4, https://cran.r-project.org/web/packages/quaqcr. Accessed 27 Oct. 2026.
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Full quaqcr package functions and examples
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