Package: RUVSeq 1.47.0

Davide Risso

RUVSeq: Remove Unwanted Variation from RNA-Seq Data

This package implements the remove unwanted variation (RUV) methods of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.

Authors:Davide Risso [aut, cre, cph], Sandrine Dudoit [aut], Lorena Pantano [ctb], Kamil Slowikowski [ctb]

RUVSeq_1.47.0.tar.gz
RUVSeq_1.47.0.zip(r-4.7)RUVSeq_1.47.0.zip(r-4.6)RUVSeq_1.47.0.zip(r-4.5)
RUVSeq_1.47.0.tgz(r-4.6-any)RUVSeq_1.47.0.tgz(r-4.5-any)
RUVSeq_1.47.0.tar.gz(r-4.7-any)RUVSeq_1.47.0.tar.gz(r-4.6-any)
RUVSeq_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RUVSeq/json (API)
NEWS

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

Bug tracker:https://github.com/drisso/ruvseq/issues

On BioConductor:RUVSeq-1.47.0(bioc 3.24)RUVSeq-1.46.0(bioc 3.23)

immunooncologydifferentialexpressionpreprocessingrnaseqsoftware

10.10 score 15 stars 5 packages 606 scripts 1.5k downloads 91 mentions 4 exports 109 dependencies

Last updated from:3265354425. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR222
linux-devel-x86_64NOTE437
source / vignettesOK292
linux-release-x86_64NOTE459
macos-release-arm64NOTE282
macos-oldrel-arm64NOTE335
windows-develNOTE355
windows-releaseNOTE332
windows-oldrelNOTE376
wasm-releaseOK181

Exports:makeGroupsRUVgRUVrRUVs

Dependencies:abindAnnotationDbiaroma.lightaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydeldirdplyrEDASeqedgeRfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2hwriterinterpIRangesjpegjsonliteKEGGRESTlambda.rlatticelatticeExtralifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfoShortReadsnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXMLxml2XVectoryaml

RUVSeq: Remove Unwanted Variation from RNA-Seq Data

Davide Risso

Rendered fromRUVSeq.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-11-22
Started: 2022-11-22

Readme and manuals

Help Manual

Help pageTopics
Remove Unwanted Variation from RNA-Seq DataRUVSeq-package RUVSeq
Make a matrix suitable for use with RUVSeq methods such as 'RUVs'.makeGroups
Deviance and Pearson Residuals for the Negative Binomial Model of 'edgeR'residuals.DGEGLM
Remove Unwanted Variation Using Control GenesRUVg RUVg,matrix,ANY,numeric-method RUVg,SeqExpressionSet,character,numeric-method RUVg-methods
Remove Unwanted Variation Using ResidualsRUVr RUVr,matrix,ANY,numeric,matrix-method RUVr,SeqExpressionSet,character,numeric,matrix-method RUVr-methods
Remove Unwanted Variation Using Replicate/Negative Control SamplesRUVs RUVs,matrix,ANY,numeric,matrix-method RUVs,SeqExpressionSet,character,numeric,matrix-method RUVs-methods