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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 (3.18)

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>

Citation (from within R, enter citation("qrqc")):

Installation

To install this package, start R (version "4.3") 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

Reference Manual PDF

Details

biocViews DataImport, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version 1.55.1
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
Linking To Rhtslib(>= 1.15.3)
Suggests
System Requirements GNU make
Enhances
URL http://github.com/vsbuffalo/qrqc
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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/
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