Polyfit

DOI: 10.18129/B9.bioc.Polyfit    

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

Bioconductor version: Release (3.11)

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 "4.0") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Polyfit")

 

PDF	R Script	Polyfit
PDF		Reference Manual

Details

biocViews	DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.22.0
In Bioconductor since	BioC 3.0 (R-3.1) (6 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	Polyfit_1.22.0.tar.gz
Windows Binary	Polyfit_1.22.0.zip
macOS 10.13 (High Sierra)	Polyfit_1.22.0.tgz
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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive