qrqc

DOI: 10.18129/B9.bioc.qrqc  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of qrqc; for the stable release version, see qrqc.

Quick Read Quality Control

Bioconductor version: Development (3.19)

Quickly scans reads and gathers statistics on base and quality frequencies, read length, k-mers by position, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected.

Author: Vince Buffalo

Maintainer: Vince Buffalo <vsbuffalo at ucdavis.edu>

Installation

To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("qrqc")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	DataImport, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version	1.56.0
In Bioconductor since	BioC 2.8 (R-2.13) (12.5 years)
License	GPL (>=2)
Depends	reshape, ggplot2, Biostrings, biovizBase, brew, xtable, testthat
Imports	reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats
LinkingTo	Rhtslib(>= 1.15.3)
Suggests
SystemRequirements	GNU make
Enhances
URL	http://github.com/vsbuffalo/qrqc
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/qrqc
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/qrqc
Package Short Url	https://bioconductor.org/packages/qrqc/
Package Downloads Report	Download Stats