Overview | A typical differential expression analysis workflow | Filtering and exploratory data analysis | RUVg: Estimating the factors of unwanted variation using control genes | Differential expression analysis | Empirical control genes | Differential expression analysis with DESeq2 | RUVs: Estimating the factors of unwanted variation using replicate samples} | RUVr: Estimating the factors of unwanted variation using residuals | Session info | References
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:
RUVSeq_1.47.0.tar.gz
RUVSeq_1.47.0.zip(r-4.7-any)RUVSeq_1.47.0.zip(r-4.6-any)RUVSeq_1.47.0.zip(r-4.5-any)
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✨
DESCRIPTION |NEWS
card.svg |card.png
RUVSeq/json (API)
| # 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
Last updated from:3265354425. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 178 | ||
| linux-devel | NOTE | 384 | ||
| source / vignettes | OK | 337 | ||
| linux-release | NOTE | 378 | ||
| macos-release | NOTE | 261 | ||
| macos-oldrel | NOTE | 256 | ||
| windows-devel | NOTE | 208 | ||
| windows-release | NOTE | 238 | ||
| windows-oldrel | NOTE | 263 | ||
| wasm-release | OK | 139 |
Exports:makeGroupsRUVgRUVrRUVs
Dependencies:AnnotationDbiaroma.lightaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrdeldirdigestdplyrEDASeqedgeRfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2hwriterinterpIRangesjpegjsonliteKEGGRESTlambda.rlatticelatticeExtralifecyclelimmamagrittrMASSmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrpwalignR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4VectorsSeqinfoShortReadsnowstatmodstringistringrsystibbletidyrtidyselectutf8vctrswithrXMLxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Remove Unwanted Variation from RNA-Seq Data | RUVSeq-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 Genes | RUVg RUVg,matrix,ANY,numeric-method RUVg,SeqExpressionSet,character,numeric-method RUVg-methods |
| Remove Unwanted Variation Using Residuals | RUVr RUVr,matrix,ANY,numeric,matrix-method RUVr,SeqExpressionSet,character,numeric,matrix-method RUVr-methods |
| Remove Unwanted Variation Using Replicate/Negative Control Samples | RUVs RUVs,matrix,ANY,numeric,matrix-method RUVs,SeqExpressionSet,character,numeric,matrix-method RUVs-methods |