RNAshapeQC

This is the development version of RNAshapeQC; to use it, please install the devel version of Bioconductor.

RNA Coverage-Shape-Based Quality Control Metrics

Bioconductor version: Development (3.23)

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.

Author: Miyeon Yeon [aut, cre, cph] ORCID: 0000-0003-1618-0643 , Won-Young Choi [aut, cph] ORCID: 0009-0003-8276-2235 , Jin Young Lee [ctb] ORCID: 0000-0002-5366-7488 , Katherine A. Hoadley [aut] ORCID: 0000-0002-1216-477X , D. Neil Hayes [aut, fnd, cph] ORCID: 0000-0001-6203-7771 , Hyo Young Choi [aut, cph] ORCID: 0000-0002-7627-8493

Maintainer: Miyeon Yeon <myeon at uthsc.edu>

Citation (from within R, enter citation("RNAshapeQC")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RNAshapeQC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RNAshapeQC")

RNAshapeQC: Quick Start Tutorial	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, QualityControl, RNASeq, Sequencing, Software, Transcriptomics
Version	0.99.10
In Bioconductor since	BioC 3.23 (R-4.6)
License	MIT + file LICENSE
Depends	R (>= 4.4)
Imports	GenomicRanges, IRanges, Rsamtools, foreach, zoo, ggplot2, dplyr, magrittr, tidyr, ComplexHeatmap, circlize, dendextend, DescTools, ggpubr, MASS, SummarizedExperiment, BiocParallel
System Requirements
URL	https://github.com/hyochoi/RNAshapeQC
Bug Reports	https://github.com/hyochoi/RNAshapeQC/issues

Suggests	doParallel, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), PupillometryR, matrixStats, RColorBrewer, scales, tibble, patchwork, ConsensusClusterPlus
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RNAshapeQC_0.99.10.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (big-sur-arm64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/RNAshapeQC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RNAshapeQC
Bioc Package Browser	https://code.bioconductor.org/browse/RNAshapeQC/
Package Short Url	https://bioconductor.org/packages/RNAshapeQC/
Package Downloads Report	Download Stats