RNAshapeQC
This is the released version of RNAshapeQC; for the devel version, see RNAshapeQC.
RNA Coverage-Shape-Based Quality Control Metrics
Bioconductor version: Release (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]
, 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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.0.0 |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RNAshapeQC_1.0.0.tar.gz |
| Windows Binary (x86_64) | RNAshapeQC_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | RNAshapeQC_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | RNAshapeQC_1.0.0.tgz |
| 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 |