Package: RNAshapeQC 1.1.0

Miyeon Yeon

RNAshapeQC: RNA Coverage-Shape-Based Quality Control Metrics

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.

Authors: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]

RNAshapeQC_1.1.0.tar.gz
RNAshapeQC_1.1.0.zip(r-4.7)RNAshapeQC_1.1.0.zip(r-4.6)RNAshapeQC_1.1.0.zip(r-4.5)
RNAshapeQC_1.1.0.tgz(r-4.6-any)RNAshapeQC_1.1.0.tgz(r-4.5-any)
RNAshapeQC_1.1.0.tar.gz(r-4.7-any)RNAshapeQC_1.1.0.tar.gz(r-4.6-any)
RNAshapeQC_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RNAshapeQC/json (API)

# Install 'RNAshapeQC' in R:

install.packages('RNAshapeQC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hyochoi/rnashapeqc/issues

Datasets:

TOY_mrna_mat - Toy mRNA-seq-like dataset for RNAshapeQC
TOY_mrna_se - Toy mRNA-seq-like dataset for RNAshapeQC
TOY_total_mat - Toy total RNA-seq-like dataset for RNAshapeQC
TOY_total_se - Toy total RNA-seq-like dataset for RNAshapeQC

On BioConductor:RNAshapeQC-1.1.0(bioc 3.24)RNAshapeQC-1.0.0(bioc 3.23)

rnaseq qualitycontrol coverage transcriptomics sequencing

5.11 score 2 stars 1 scripts 226 downloads 24 exports 151 dependencies

Last updated from:a24cfa2e3c. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	220
linux-devel-x86_64	OK	376
source / vignettes	OK	325
linux-release-x86_64	OK	270
macos-release-arm64	OK	156
macos-oldrel-arm64	OK	198
windows-devel	OK	176
windows-release	OK	176
windows-oldrel	OK	176
wasm-release	OK	205

Exports:.build_pileupExon combine_vecObj compute_DIIwt compute_DR compute_MCD compute_SOI compute_wCV construct_pileup extract_RData filter_lowExpGenes gen_DR gen_MCD gen_wCV get_DIIhc get_DIIwt get_DR get_MCD get_pileupExon get_SOI get_wCV plot_DIIwt plot_GBC plot_GBCos plot_SOI

Dependencies:abind askpass backports BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops boot broom car carData cellranger circlize class cli clipr clue cluster codetools colorspace ComplexHeatmap corrplot cowplot cpp11 crayon curl data.table DelayedArray dendextend Deriv DescTools digest doBy doParallel dplyr e1071 Exact expm farver forcats foreach forecast formatR Formula fracdiff fs futile.logger futile.options generics GenomicRanges GetoptLong ggplot2 ggpubr ggrepel ggsci ggsignif gld GlobalOptions glue gridExtra gtable haven hms httr IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle lme4 lmom lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv mime minqa modelr mvtnorm nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig png polynom prettyunits progress proxy purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr readxl reformulas rematch Rhtslib rjson rlang rootSolve Rsamtools rstatix rstudioapi S4Arrays S4Vectors S7 scales Seqinfo shape snow SparseArray SparseM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate tzdb urca utf8 vctrs viridis viridisLite vroom withr XVector zoo

RNAshapeQC: Quick Start Tutorial

Rendered fromRNAshapeQC_intro.Rmdusingknitr::rmarkdown

Last update: 2026-03-21
Started: 2025-12-01

Help page	Topics
Core helper to build exon-only pileup	.build_pileupExon
Combine vectors as a matrix from objects	combine_vecObj
Core helper to compute a degraded/intact index using gene weight	compute_DIIwt
Core helper to compute decay rate	compute_DR
Core helper to compute a mean coverage depth	compute_MCD
Core helper to compute a suboptimal/optimal index	compute_SOI
Core helper to compute a window coefficient of variation	compute_wCV
Construct a per-gene pileup from BAM files (for single-study or multi-study)	construct_pileup
Extract an object from .RData	extract_RData
Filter low expressed genes	filter_lowExpGenes
Get a decay rate for genes and samples (for a single gene)	gen_DR
Get a mean coverage depth for genes and samples (for a single gene)	gen_MCD
Get a window coefficient of variation for genes and samples (for a single gene)	gen_wCV
Get a degraded/intact index for samples using hierarchical clustering	get_DIIhc
Get a degraded/intact index for samples using gene weight	get_DIIwt
Get a decay rate for genes and samples (for a genelist)	get_DR
Get a mean coverage depth for genes and samples (for a genelist)	get_MCD
Get a focused pileup of exon location (for single-study)	get_pileupExon
Get a suboptimal/optimal index for samples	get_SOI
Get a window coefficient of variation for genes and samples (for a genelist)	get_wCV
Plot degraded/intact index outputs	plot_DIIwt
Plot gene body coverage	plot_GBC
Plot gene body coverage with optimal samples	plot_GBCos
Plot suboptimal/optimal index outputs	plot_SOI
Toy mRNA-seq-like dataset for RNAshapeQC (matrix input)	TOY_mrna_mat
Toy mRNA-seq-like dataset for RNAshapeQC (SE input)	TOY_mrna_se
Toy total RNA-seq-like dataset for RNAshapeQC (matrix input)	TOY_total_mat
Toy total RNA-seq-like dataset for RNAshapeQC (SE input)	TOY_total_se

Package: RNAshapeQC 1.1.0

RNAshapeQC: RNA Coverage-Shape-Based Quality Control Metrics

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