RNAshapeQC
This is the development version of RNAshapeQC; for the stable release version, see RNAshapeQC.
RNA Coverage-Shape-Based Quality Control Metrics
Bioconductor version: Development (3.24)
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] 
, Won-Young Choi [aut, cph] , Jin Young Lee [ctb] , Katherine A. Hoadley [aut] , D. Neil Hayes [aut, fnd, cph] , Hyo Young Choi [aut, cph]
Maintainer: Miyeon Yeon <myeon at uthsc.edu>
citation("RNAshapeQC")):Miyeon Yeon, Won-Young Choi, Katherine A. Hoadley, D. Neil Hayes, Hyo Young Choi. RNAshapeQC: RNA Coverage-Shape-Based Quality Control Metrics. doi:10.18129/B9.bioc.RNAshapeQC, R package version 1.1.0, https://bioconductor.org/packages/RNAshapeQC.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, QualityControl, RNASeq, Sequencing, Software, Transcriptomics |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| 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 |
See More
| Suggests | doParallel, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), PupillometryR, matrixStats, RColorBrewer, scales, tibble, patchwork, ConsensusClusterPlus |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RNAshapeQC_1.1.0.tar.gz |
| Windows Binary (x86_64) | RNAshapeQC_1.1.0.zip |
| macOS Binary (big-sur-x86_64) | RNAshapeQC_1.1.0.tgz |
| macOS Binary (sonoma-arm64) | RNAshapeQC_1.1.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RNAshapeQC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RNAshapeQC |
| Package Short Url | https://bioconductor.org/packages/RNAshapeQC/ |
| Package Downloads Report | Download Stats |