qrqc

DOI: 10.18129/B9.bioc.qrqc    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see qrqc.

Quick Read Quality Control

Bioconductor version: 3.8

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("qrqc")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("qrqc")

 

PDF	R Script	Using the qrqc package to gather information about sequence qualities
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version	1.36.0
In Bioconductor since	BioC 2.8 (R-2.13) (8 years)
License	GPL (>=2)
Depends	reshape, ggplot2, Biostrings, biovizBase, brew, xtable, Rsamtools(>= 1.19.38), testthat
Imports	reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats
LinkingTo	Rsamtools
Suggests
SystemRequirements
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	qrqc_1.36.0.tar.gz
Windows Binary	qrqc_1.36.0.zip
Mac OS X 10.11 (El Capitan)	qrqc_1.36.0.tgz
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	http://bioconductor.org/packages/qrqc/
Package Downloads Report	Download Stats