Package: RNAshapeQC 1.0.0

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_1.0.0.tar.gz
RNAshapeQC_1.0.0.zip(r-4.7)RNAshapeQC_1.0.0.zip(r-4.6)RNAshapeQC_1.0.0.zip(r-4.5)
RNAshapeQC_1.0.0.tgz(r-4.6-any)RNAshapeQC_1.0.0.tgz(r-4.5-any)
RNAshapeQC_1.0.0.tar.gz(r-4.7-any)RNAshapeQC_1.0.0.tar.gz(r-4.6-any)
RNAshapeQC_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RNAshapeQC/json (API)
NEWS

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

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

Datasets:

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

rnaseqqualitycontrolcoveragetranscriptomicssequencing

5.11 score 2 stars 266 downloads 24 exports 152 dependencies

Last updated from:5d1a8e43dc (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE175
linux-devel-x86_64OK278
source / vignettesOK280
linux-release-x86_64OK277
macos-release-arm64OK187
macos-oldrel-arm64OK153
windows-develOK173
windows-releaseOK186
windows-oldrelOK175
wasm-releaseOK177

Exports:.build_pileupExoncombine_vecObjcompute_DIIwtcompute_DRcompute_MCDcompute_SOIcompute_wCVconstruct_pileupextract_RDatafilter_lowExpGenesgen_DRgen_MCDgen_wCVget_DIIhcget_DIIwtget_DRget_MCDget_pileupExonget_SOIget_wCVplot_DIIwtplot_GBCplot_GBCosplot_SOI

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsbootbroomcarcarDatacellrangercirclizeclassclicliprclueclustercodetoolscolorspaceComplexHeatmapcorrplotcowplotcpp11crayoncurldata.tableDelayedArraydendextendDerivDescToolsdigestdoBydoParalleldplyre1071ExactexpmfarverforcatsforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsGenomicRangesGetoptLongggplot2ggpubrggrepelggsciggsignifgldGlobalOptionsgluegridExtragtablehavenhmshttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelme4lmomlmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigpngpolynomprettyunitsprogressproxypurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreadxlreformulasrematchRhtslibrjsonrlangrootSolveRsamtoolsrstatixrstudioapiS4ArraysS4VectorsS7scalesSeqinfoshapesnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimeDatetzdburcautf8vctrsviridisviridisLitevroomwithrXVectorzoo

RNAshapeQC: Quick Start Tutorial

Miyeon Yeon, Won-Young Choi, and Hyo Young Choi

Rendered fromRNAshapeQC_intro.Rmdusingknitr::rmarkdownon May 30 2026.

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

Readme and manuals

Help Manual

Help pageTopics
Core helper to build exon-only pileup.build_pileupExon
Combine vectors as a matrix from objectscombine_vecObj
Core helper to compute a degraded/intact index using gene weightcompute_DIIwt
Core helper to compute decay ratecompute_DR
Core helper to compute a mean coverage depthcompute_MCD
Core helper to compute a suboptimal/optimal indexcompute_SOI
Core helper to compute a window coefficient of variationcompute_wCV
Construct a per-gene pileup from BAM files (for single-study or multi-study)construct_pileup
Extract an object from .RDataextract_RData
Filter low expressed genesfilter_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 clusteringget_DIIhc
Get a degraded/intact index for samples using gene weightget_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 samplesget_SOI
Get a window coefficient of variation for genes and samples (for a genelist)get_wCV
Plot degraded/intact index outputsplot_DIIwt
Plot gene body coverageplot_GBC
Plot gene body coverage with optimal samplesplot_GBCos
Plot suboptimal/optimal index outputsplot_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