Package: gDNAx
Type: Package
Title: Diagnostics for assessing genomic DNA contamination in RNA-seq
        data
Version: 1.4.0
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, 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
RoxygenNote: 7.3.1
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: RELEASE_3_20
git_last_commit: 677cebe
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: no
Packaged: 2024-10-30 00:48:54 UTC; biocbuild
Author: Beatriz Calvo-Serra [aut],
  Robert Castelo [aut, cre]
Maintainer: Robert Castelo <robert.castelo@upf.edu>
Built: R 4.4.2; ; 2025-01-03 18:33:16 UTC; unix
