SVAPLSseq: SVAPLSseq-An R package to adjust for the hidden factors of variability in differential gene expression studies based on RNAseq data

The package contains functions that are intended for the identification of differentially expressed genes between two groups of samples from RNAseq data after adjusting for various hidden biological and technical factors of variability.

Author
Sutirtha Chakraborty
Date of publication
None
Maintainer
Sutirtha Chakraborty <sutirtha_sutir@yahoo.co.in>
License
GPL-3
Version
1.0.0

View on Bioconductor

Man pages

prop.vars
Accessor for the 'prop.vars' slot of a 'svplsSurr' object
pvs.adj
Accessor for the 'pvs.adj' slot of a 'svplsTest' object
pvs.unadj
Accessor for the 'pvs.unadj' slot of a 'svplsTest' object
sig.genes
Accessor for the 'sig.genes' slot of a 'svplsTest' object
sim.dat
A simulated RNAseq gene expression count data affected by...
surr
Accessor for the 'surr' slot of a 'svplsSurr' object
SVAPLSseq-package
SVAPLSseq: An R package to adjust for the hidden factors of...
svplsSurr
svplsSurr
svplsSurr-class
svplsSurr
svplsTest
svplsTest
svplsTest-class
svplsTest

Files in this package

SVAPLSseq/DESCRIPTION
SVAPLSseq/NAMESPACE
SVAPLSseq/NEWS
SVAPLSseq/R
SVAPLSseq/R/AllClasses.R
SVAPLSseq/R/AllGenerics.R
SVAPLSseq/R/Methods.R
SVAPLSseq/R/svplsSurr.R
SVAPLSseq/R/svplsTest.R
SVAPLSseq/README.md
SVAPLSseq/build
SVAPLSseq/build/vignette.rds
SVAPLSseq/data
SVAPLSseq/data/sim.dat.rda
SVAPLSseq/inst
SVAPLSseq/inst/doc
SVAPLSseq/inst/doc/SVAPLSseq.R
SVAPLSseq/inst/doc/SVAPLSseq.Rnw
SVAPLSseq/inst/doc/SVAPLSseq.pdf
SVAPLSseq/man
SVAPLSseq/man/SVAPLSseq-package.Rd
SVAPLSseq/man/prop.vars.Rd
SVAPLSseq/man/pvs.adj.Rd
SVAPLSseq/man/pvs.unadj.Rd
SVAPLSseq/man/sig.genes.Rd
SVAPLSseq/man/sim.dat.Rd
SVAPLSseq/man/surr.Rd
SVAPLSseq/man/svplsSurr-class.Rd
SVAPLSseq/man/svplsSurr.Rd
SVAPLSseq/man/svplsTest-class.Rd
SVAPLSseq/man/svplsTest.Rd
SVAPLSseq/vignettes
SVAPLSseq/vignettes/SVAPLSseq.Rnw