Polyfit: Add-on to DESeq to improve p-values and q-values

Polyfit is an add-on to the packages DESeq which ensures the p-value distribution is uniform over the interval [0, 1] for data satisfying the null hypothesis of no differential expression, and uses an adpated Storey-Tibshiran method to calculate q-values.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Polyfit")
AuthorConrad Burden
Bioconductor views DifferentialExpression GeneExpression RNASeq Sequencing
Date of publicationNone
MaintainerConrad Burden <conrad.burden@anu.edu.au>
LicenseGPL (>= 3)
Version1.10.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/PolyfitFunctions.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/polyfit.R
inst/doc/polyfit.Rnw
inst/doc/polyfit.pdf
man
man/Polyfit-package.Rd man/levelPValues.Rd man/pfNbinomTest.Rd man/twoSidedPValueFromDiscrete.Rd
vignettes
vignettes/polyfit.Rnw
vignettes/polyfitFig1.pdf
vignettes/polyfitFig4.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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