Type: Package
Package: CleanUpRNAseq
Title: Detect and Correct Genomic DNA Contamination in RNA-seq Data
Version: 1.4.0
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, Seqinfo, 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
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:31:19 UTC
RemoteUrl: https://github.com/bioc/CleanUpRNAseq
RemoteRef: RELEASE_3_22
RemoteSha: 3ccdf23da922bf76fb57aeed0a5fa7dae09fc06d
NeedsCompilation: no
Packaged: 2026-01-25 08:05:22 UTC; root
Author: Haibo Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-4213-2883>),
  Kevin O'Connor [ctb],
  Michelle Kelliher [ctb],
  Lihua Julie Zhu [aut],
  Kai Hu [aut]
Maintainer: Haibo Liu <haibo.liu@umassmed.edu>
Built: R 4.5.2; ; 2026-01-25 08:08:45 UTC; windows
