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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
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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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, Infrastructure, QualityControl, Sequencing, Software |
| Version | 1.0.1 |
| In Bioconductor since | BioC 3.5 (R-3.4) (0.5 years) |
| 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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