Package: basecallQC
Type: Package
Title: Working with Illumina Basecalling and Demultiplexing input and
        output files
Version: 1.28.0
Author: Thomas Carroll and Marian Dore
Maintainer: Thomas Carroll <tc.infomatics@gmail.com>
Description: 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.
biocViews: Sequencing, Infrastructure, DataImport, QualityControl
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
Suggests: testthat, BiocStyle
VignetteBuilder: knitr
SystemRequirements: bcl2Fastq (versions >= 2.1.7)
Collate: processIlluminaSamplesheets_Functions.R
        processXMLs_Functions.R allClasses.R allMethods.R
        processExternalFormats_Functions.R plots.R reporting.R tables.R
        FastQCShortRead_Functions.R processInterOps_Functions.R
RoxygenNote: 7.1.0
git_url: https://git.bioconductor.org/packages/basecallQC
git_branch: RELEASE_3_19
git_last_commit: 536aad0
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-01 21:11:25 UTC; biocbuild
Built: R 4.4.0; ; 2024-05-02 12:27:15 UTC; windows
