To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("basecallQC")

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

basecallQC

DOI: 10.18129/B9.bioc.basecallQC    

Working with Illumina Basecalling and Demultiplexing input and output files

Bioconductor version: Release (3.5)

The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

Author: Thomas Carroll and Marian Dore

Maintainer: Thomas Carroll <tc.infomatics at gmail.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("basecallQC")

Documentation

HTML R Script Vignette Title
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, Infrastructure, QualityControl, Sequencing, Software
Version 1.0.1
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
License GPL (>= 3)
Depends R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml
Imports ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead
LinkingTo
Suggests testthat, BiocStyle
SystemRequirements bcl2Fastq (versions >= 2.1.7)
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package basecallQC_1.0.1.tar.gz
Windows Binary basecallQC_1.0.1.zip
Mac OS X 10.11 (El Capitan) basecallQC_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/basecallQC
Package Short Url http://bioconductor.org/packages/basecallQC/
Package Downloads Report Download Stats

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