Package: basecallQC
Type: Package
Title: Working with Illumina Basecalling and Demultiplexing input and
        output files
Version: 1.35.0
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
Config/pak/sysreqs: libgdal-dev gdal-bin libgeos-dev make libbz2-dev
        libicu-dev libjpeg-dev liblzma-dev libpng-dev libxml2-dev
        libproj-dev libsqlite3-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:38:02 UTC
RemoteUrl: https://github.com/bioc/basecallQC
RemoteRef: HEAD
RemoteSha: f54574acd785e2cfae500638bdc07a2a5f7e0e3f
NeedsCompilation: no
Packaged: 2025-11-02 14:41:44 UTC; root
Built: R 4.6.0; ; 2025-11-02 14:44:19 UTC; windows
