Polyfit

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see Polyfit.

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


Bioconductor version: 3.13

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.

Author: Conrad Burden

Maintainer: Conrad Burden <conrad.burden at anu.edu.au>

Citation (from within R, enter citation("Polyfit")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Polyfit")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.26.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL (>= 3)
Depends DESeq
Imports
System Requirements
URL
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/Polyfit
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Polyfit
Package Short Url https://bioconductor.org/packages/Polyfit/
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Old Source Packages for BioC 3.13 Source Archive