RUVSeq: Remove Unwanted Variation from RNA-Seq Data

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

Author
Davide Risso [aut, cre, cph], Sandrine Dudoit [aut], Lorena Pantano [ctb], Kamil Slowikowski [ctb]
Date of publication
None
Maintainer
Davide Risso <risso.davide@gmail.com>
License
Artistic-2.0
Version
1.8.0
URLs

View on Bioconductor

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

Files in this package

RUVSeq/DESCRIPTION
RUVSeq/NAMESPACE
RUVSeq/R
RUVSeq/R/AllGenerics.R
RUVSeq/R/RUVg-methods.R
RUVSeq/R/RUVr-methods.R
RUVSeq/R/RUVs-methods.R
RUVSeq/R/helper.R
RUVSeq/R/residuals.DGEGLM.R
RUVSeq/build
RUVSeq/build/vignette.rds
RUVSeq/inst
RUVSeq/inst/CITATION
RUVSeq/inst/NEWS
RUVSeq/inst/doc
RUVSeq/inst/doc/RUVSeq.R
RUVSeq/inst/doc/RUVSeq.Rnw
RUVSeq/inst/doc/RUVSeq.pdf
RUVSeq/man
RUVSeq/man/RUVSeq-package.Rd
RUVSeq/man/RUVg.Rd
RUVSeq/man/RUVr.Rd
RUVSeq/man/RUVs.Rd
RUVSeq/man/makeGroups.Rd
RUVSeq/man/residuals.DGEGLM.Rd
RUVSeq/tests
RUVSeq/tests/RUVg.R
RUVSeq/tests/RUVr.R
RUVSeq/tests/RUVs.R
RUVSeq/vignettes
RUVSeq/vignettes/RUVSeq.Rnw
RUVSeq/vignettes/biblio.bib