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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 package is for version 3.18 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see qrqc.

Quick Read Quality Control


Bioconductor version: Release (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")

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 1.56.0
In Bioconductor since BioC 2.8 (R-2.13) (13 years)
License GPL (>=2)
Depends reshape, ggplot2, Biostrings, biovizBase, brew, xtable, testthat
Imports reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats
System Requirements GNU make
URL http://github.com/vsbuffalo/qrqc
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Linking To Rhtslib(>= 1.15.3)
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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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