Package: RNAshapeQC
Type: Package
Title: RNA Coverage-Shape-Based Quality Control Metrics
Version: 0.99.10
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
git_url: https://git.bioconductor.org/packages/RNAshapeQC
git_branch: devel
git_last_commit: fefca97
git_last_commit_date: 2026-03-25
Repository: Bioconductor 3.24
Date/Publication: 2026-04-20
NeedsCompilation: no
Packaged: 2026-04-21 00:24:11 UTC; biocbuild
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>
