RUVSeq: Remove Unwanted Variation from RNA-Seq Data
Version 1.10.0

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

AuthorDavide Risso [aut, cre, cph], Sandrine Dudoit [aut], Lorena Pantano [ctb], Kamil Slowikowski [ctb]
Bioconductor views DifferentialExpression Preprocessing RNASeq Software
Date of publicationNone
MaintainerDavide Risso <risso.davide@gmail.com>
LicenseArtistic-2.0
Version1.10.0
URL https://github.com/drisso/RUVSeq
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RUVSeq")

Getting started

Package overview

Popular man pages

makeGroups: Make a matrix suitable for use with RUVSeq methods such as...
residuals.DGEGLM: Deviance and Pearson Residuals for the Negative Binomial...
RUVg: Remove Unwanted Variation Using Control Genes
RUVr: Remove Unwanted Variation Using Residuals
RUVs: Remove Unwanted Variation Using Replicate/Negative Control...
RUVSeq-package: Remove Unwanted Variation from RNA-Seq Data
See all...

All man pages Function index File listing

Man pages

makeGroups: Make a matrix suitable for use with RUVSeq methods such as...
residuals.DGEGLM: Deviance and Pearson Residuals for the Negative Binomial...
RUVg: Remove Unwanted Variation Using Control Genes
RUVr: Remove Unwanted Variation Using Residuals
RUVs: Remove Unwanted Variation Using Replicate/Negative Control...
RUVSeq-package: Remove Unwanted Variation from RNA-Seq Data

Functions

RUVSeq Man page
RUVSeq-package Man page
RUVg Man page
RUVg,SeqExpressionSet,character,numeric-method Man page
RUVg,matrix,ANY,numeric-method Man page
RUVg-methods Man page
RUVr Man page
RUVr,SeqExpressionSet,character,numeric,matrix-method Man page
RUVr,matrix,ANY,numeric,matrix-method Man page
RUVr-methods Man page
RUVs Man page
RUVs,SeqExpressionSet,character,numeric,matrix-method Man page
RUVs,matrix,ANY,numeric,matrix-method Man page
RUVs-methods Man page
makeGroups Man page Source code
residuals.DGEGLM Man page Source code
sWholeNumber Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllGenerics.R
R/RUVg-methods.R
R/RUVr-methods.R
R/RUVs-methods.R
R/helper.R
R/residuals.DGEGLM.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/RUVSeq.R
inst/doc/RUVSeq.Rnw
inst/doc/RUVSeq.pdf
man
man/RUVSeq-package.Rd
man/RUVg.Rd
man/RUVr.Rd
man/RUVs.Rd
man/makeGroups.Rd
man/residuals.DGEGLM.Rd
tests
tests/RUVg.R
tests/RUVr.R
tests/RUVs.R
vignettes
vignettes/RUVSeq.Rnw
vignettes/biblio.bib
RUVSeq documentation built on May 20, 2017, 10:37 p.m.