DESCRIPTION

Type: Package
Package: CleanUpRNAseq
Title: Detect and Correct Genomic DNA Contamination in RNA-seq Data
Version: 1.1.1
Authors@R: c(
    person("Haibo", "Liu", , "haibo.liu@umassmed.edu", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-4213-2883")),
    person("Kevin", "O'Connor", , "Kevin.O'Connor@umassmed.edu", role = "ctb"),
    person("Michelle", "Kelliher", , "Michelle.Kelliher@umassmed.edu", role = "ctb"),
    person("Lihua Julie", "Zhu", , "Julie.Zhu@umassmed.edu", role = "aut"),
    person("Kai", "Hu", , "kai.hu@umassmed.edu", role = "aut")
  )
Description: RNA-seq data generated by some library preparation methods,
    such as rRNA-depletion-based method and the SMART-seq method, might be
    contaminated by genomic DNA (gDNA), if DNase I disgestion is not
    performed properly during RNA preparation. CleanUpRNAseq is developed
    to check if RNA-seq data is suffered from gDNA contamination. If so,
    it can perform correction for gDNA contamination and reduce false
    discovery rate of differentially expressed genes.
License: GPL-3
BugReports: https://github.com/haibol2016/CleanUpRNAseq/issues
Depends: 
    R (>= 4.4.0)
Imports: 
    AnnotationFilter,
    BiocGenerics,
    Biostrings,
    BSgenome,
    DESeq2,
    edgeR,
    ensembldb,
    GenomeInfoDb,
    GenomicRanges,
    ggplot2,
    ggrepel,
    graphics,
    grDevices,
    KernSmooth,
    limma,
    methods,
    pheatmap,
    qsmooth,
    R6,
    RColorBrewer,
    Rsamtools,
    Rsubread,
    reshape2,
    SummarizedExperiment,
    stats,
    tximport,
    utils
Suggests: 
    BiocStyle,
    BSgenome.Hsapiens.UCSC.hg38,
    EnsDb.Hsapiens.v86,
    ggplotify,
    knitr,
    patchwork,
    R.utils,
    rmarkdown,
    testthat (>= 3.0.0)
VignetteBuilder: 
    knitr
biocViews: QualityControl, Sequencing, GeneExpression
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Collate: 
    'CleanUpRNAseq-package.R'
    'R6_class.R'
    'misc.R'
    'check_gDNA.R'
    'correction_methods.R'
    'data.R'
Config/testthat/edition: 3