Package: RUVSeq 1.41.0

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_1.41.0.tar.gz
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RUVSeq_1.41.0.tgz(r-4.4-any)RUVSeq_1.41.0.tgz(r-4.3-any)
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RUVSeq.pdf |RUVSeq.html✨
RUVSeq/json (API)
NEWS

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

Peer review:

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

On BioConductor:RUVSeq-1.41.0(bioc 3.21)RUVSeq-1.40.0(bioc 3.20)

immunooncologydifferentialexpressionpreprocessingrnaseqsoftware

9.87 score 12 stars 5 packages 486 scripts 1.4k downloads 91 mentions 4 exports 113 dependencies

Last updated 2 months agofrom:bb9c230ec8. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winNOTEDec 18 2024
R-4.5-linuxNOTEDec 18 2024
R-4.4-winNOTEDec 18 2024
R-4.4-macNOTEDec 18 2024
R-4.3-winNOTEDec 18 2024
R-4.3-macNOTEDec 18 2024

Exports:makeGroupsRUVgRUVrRUVs

Dependencies:abindAnnotationDbiaroma.lightaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydeldirdigestdplyrEDASeqedgeRfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2hwriterinterpIRangesjpegjsonliteKEGGRESTlambda.rlatticelatticeExtralifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsShortReadsnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLxml2XVectoryamlzlibbioc

RUVSeq: Remove Unwanted Variation from RNA-Seq Data

Davide Risso

Rendered fromRUVSeq.Rmdusingknitr::rmarkdownon Dec 18 2024.

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