basecallQC
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see basecallQC.
Working with Illumina Basecalling and Demultiplexing input and output files
Bioconductor version: 3.9
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("basecallQC")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("basecallQC")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("basecallQC")| Vignette Title | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, QualityControl, Sequencing, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 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 |
| System Requirements | bcl2Fastq (versions >= 2.1.7) |
| URL |
See More
| Suggests | testthat, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | basecallQC_1.8.0.tar.gz |
| Windows Binary | basecallQC_1.8.0.zip |
| Mac OS X 10.11 (El Capitan) | basecallQC_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/basecallQC |
| Source Repository (Developer Access) | git clone [email protected]:packages/basecallQC |
| Bioc Package Browser | https://code.bioconductor.org/browse/basecallQC/ |
| Package Short Url | https://bioconductor.org/packages/basecallQC/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |