basecallQC
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 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see basecallQC.
Working with Illumina Basecalling and Demultiplexing input and output files
Bioconductor version: Release (3.23)
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")):Thomas Carroll and Marian Dore. basecallQC: Working with Illumina Basecalling and Demultiplexing input and output files. doi:10.18129/B9.bioc.basecallQC, R package version 1.35.0, https://bioconductor.org/packages/basecallQC.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | 1.35.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 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 |
| 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | basecallQC_1.35.0.tar.gz |
| Windows Binary (x86_64) | basecallQC_1.35.0.zip |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/basecallQC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/basecallQC |
| Package Short Url | https://bioconductor.org/packages/basecallQC/ |
| Package Downloads Report | Download Stats |