To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("qrqc")

In most cases, you don't need to download the package archive at all.

qrqc

Quick Read Quality Control

Bioconductor version: Release (3.0)

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 and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("qrqc")

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 1.20.0
In Bioconductor since BioC 2.8 (R-2.13)
License GPL (>=2)
Depends reshape, ggplot2, Biostrings, biovizBase, brew, xtable, Rsamtools(>= 1.3.28), testthat
Imports reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats
Suggests
System Requirements
URL http://github.com/vsbuffalo/qrqc
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source qrqc_1.20.0.tar.gz
Windows Binary qrqc_1.20.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) qrqc_1.20.0.tgz
Mac OS X 10.9 (Mavericks) qrqc_1.20.0.tgz
Browse/checkout source (username/password: readonly)
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