Package: gDNAx
Type: Package
Title: Diagnostics for assessing genomic DNA contamination in RNA-seq data
Version: 1.9.1
Authors@R: c(
  person("Beatriz", "Calvo-Serra", email = "beatriz.calvo@upf.edu", role = c("aut")),
  person("Robert", "Castelo", email = "robert.castelo@upf.edu", role = c("aut", "cre")))
Description: Provides diagnostics for assessing genomic DNA contamination in
    RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin.
License: Artistic-2.0
Encoding: UTF-8
Depends:
    R (>= 4.3)
Imports: 
    methods,
    BiocGenerics,
    BiocParallel,
    matrixStats,
    Biostrings,
    S4Vectors,
    IRanges,
    Seqinfo,
    GenomeInfoDb,
    GenomicRanges,
    GenomicFiles,
    GenomicAlignments,
    GenomicFeatures,
    Rsamtools,
    AnnotationHub,
    RColorBrewer,
    AnnotationDbi,
    bitops,
    plotrix,
    SummarizedExperiment,
    grDevices,
    graphics,
    stats,
    utils,
    cli
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    RUnit,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    gDNAinRNAseqData
biocViews: Transcription, Transcriptomics, RNASeq, Sequencing, Preprocessing, Software, GeneExpression, Coverage, DifferentialExpression, FunctionalGenomics, SplicedAlignment, Alignment
VignetteBuilder: knitr
Roxygen: list(markdown=TRUE)
RoxygenNote: 7.3.2
URL: https://github.com/functionalgenomics/gDNAx
BugReports: https://github.com/functionalgenomics/gDNAx/issues
Collate:
    'AllGenerics.R'
    'AllClasses.R'
    'utils.R'
    'dx.R'
    'filterBAMtx.R'
    'tx.R'
    'strandedness.R'
    'gDNAx.R'
    'gDNAx-pkg-deprecated.R'
git_url: https://git.bioconductor.org/packages/gDNAx
git_branch: devel
git_last_commit: 1ac6999
git_last_commit_date: 2025-12-09
Repository: Bioconductor 3.23
