Polyfit

DOI: 10.18129/B9.bioc.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>

Installation

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

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

BiocManager::install("Polyfit")

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

Documentation

PDF		Reference Manual

Details

biocViews	DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.26.0
In Bioconductor since	BioC 3.0 (R-3.1) (7 years)
License	GPL (>= 3)
Depends	DESeq
Imports
LinkingTo
Suggests	BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

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 [email protected]:packages/Polyfit
Package Short Url	https://bioconductor.org/packages/Polyfit/
Package Downloads Report	Download Stats