Package: RNAshapeQC
Type: Package
Title: RNA Coverage-Shape-Based Quality Control Metrics
Version: 1.1.0
Authors@R: 
    c(
      person("Miyeon", "Yeon",
             email = "myeon@uthsc.edu",
             role = c("aut", "cre", "cph"),
             comment = c(ORCID = "0000-0003-1618-0643")),
      person("Won-Young", "Choi",
             email = "wchoi11@uthsc.edu",
             role = c("aut", "cph"),
             comment = c(ORCID = "0009-0003-8276-2235")),
      person("Jin Young", "Lee",
             email = "jlee307@uthsc.edu",
             role = "ctb",
             comment = c(ORCID = "0000-0002-5366-7488")),
      person("Katherine A.", "Hoadley",
             email = "hoadley@med.unc.edu",
             role = "aut",
             comment = c(ORCID = "0000-0002-1216-477X")),
      person("D. Neil", "Hayes",
             email = "Neil.Hayes@uthsc.edu",
             role = c("aut", "fnd", "cph"),
             comment = c(ORCID = "0000-0001-6203-7771")),
      person("Hyo Young", "Choi",
             email = "hyoyoung.choi@uthsc.edu",
             role = c("aut", "cph"),
             comment = c(ORCID = "0000-0002-7627-8493"))
    )
Description: RNAshapeQC provides coverage-shape-based quality control
        (QC) metrics for mRNA-seq and total RNA-seq data. It supports
        per-gene pileup construction from BAM files as well as toy
        datasets for quick-start examples. The package implements
        protocol-specific metrics, including decay rate (DR),
        degradation score (DS), mean coverage depth (MCD), window
        coefficient of variation (wCV), area under the curve (AUC), and
        shape-based sample-level indices. RNAshapeQC also includes
        HPC-friendly functions for per-gene batch processing and
        cross-study pileup generation. This package enables
        interpretable, protocol-specific QC assessments for diverse
        RNA-seq workflows.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2
Depends: R (>= 4.4)
Imports: GenomicRanges, IRanges, Rsamtools, foreach, zoo, ggplot2,
        dplyr, magrittr, tidyr, ComplexHeatmap, circlize, dendextend,
        DescTools, ggpubr, MASS, SummarizedExperiment, BiocParallel
Suggests: doParallel, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0),
        PupillometryR, matrixStats, RColorBrewer, scales, tibble,
        patchwork, ConsensusClusterPlus
biocViews: RNASeq, QualityControl, Coverage, Transcriptomics,
        Sequencing
URL: https://github.com/hyochoi/RNAshapeQC
BugReports: https://github.com/hyochoi/RNAshapeQC/issues
VignetteBuilder: knitr
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libuv1-dev libssl-dev perl libx11-dev xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:06:41 UTC
RemoteUrl: https://github.com/bioc/RNAshapeQC
RemoteRef: HEAD
RemoteSha: a24cfa2e3c13ba5946398d99c073afbeb6f1e1ed
NeedsCompilation: no
Packaged: 2026-07-18 08:29:44 UTC; root
Author: Miyeon Yeon [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-1618-0643>),
  Won-Young Choi [aut, cph] (ORCID:
    <https://orcid.org/0009-0003-8276-2235>),
  Jin Young Lee [ctb] (ORCID: <https://orcid.org/0000-0002-5366-7488>),
  Katherine A. Hoadley [aut] (ORCID:
    <https://orcid.org/0000-0002-1216-477X>),
  D. Neil Hayes [aut, fnd, cph] (ORCID:
    <https://orcid.org/0000-0001-6203-7771>),
  Hyo Young Choi [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-7627-8493>)
Maintainer: Miyeon Yeon <myeon@uthsc.edu>