Other packages > Find by keyword >

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 04 Jul. 2026.
Previous versions and publish date:
No previous versions
Other packages that cited quaqcr R package
View quaqcr citation profile
Other R packages that quaqcr depends, imports, suggests or enhances
Complete documentation for quaqcr
Functions, R codes and Examples using the quaqcr R package
Full quaqcr package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

verbalisr  
Describe Pedigree Relationships in Words
Describe in words the genealogical relationship between two members of a given pedigree, using the a ...
Download / Learn more Package Citations See dependency  
ggokabeito  
'Okabe-Ito' Scales for 'ggplot2' and 'ggraph'
Discrete scales for the colorblind-friendly 'Okabe-Ito' palette, including 'color', 'fill', and 'ed ...
Download / Learn more Package Citations See dependency  
nestfs  
Cross-Validated (Nested) Forward Selection
Implementation of forward selection based on cross-validated linear and logistic regression. ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
CDVineCopulaConditional  
Sampling from Conditional C- and D-Vine Copulas
Provides tools for sampling from a conditional copula density decomposed via Pair-Copula Constructi ...
Download / Learn more Package Citations See dependency  

27,737

R Packages

236,180

Dependencies

73,674

Author Associations

27,536

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA