Package: gDNAx
Type: Package
Title: Diagnostics for assessing genomic DNA contamination in RNA-seq
        data
Version: 1.11.0
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: 7.3.3
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'
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:01:25 UTC
RemoteUrl: https://github.com/bioc/gDNAx
RemoteRef: HEAD
RemoteSha: b94edc32cd52828080032a51dbb43c56c62dc09c
NeedsCompilation: no
Packaged: 2026-07-04 23:44:57 UTC; root
Author: Beatriz Calvo-Serra [aut],
  Robert Castelo [aut, cre]
Maintainer: Robert Castelo <robert.castelo@upf.edu>