PolySTest

This is the development version of PolySTest; to use it, please install the devel version of Bioconductor.

PolySTest: Detection of differentially regulated features. Combined statistical testing for data with few replicates and missing values


Bioconductor version: Development (3.20)

The complexity of high-throughput quantitative omics experiments often leads to low replicates numbers and many missing values. We implemented a new test to simultaneously consider missing values and quantitative changes, which we combined with well-performing statistical tests for high confidence detection of differentially regulated features. The package contains functions to run the test and to visualize the results.

Author: Veit Schwämmle [aut, cre]

Maintainer: Veit Schwämmle <veits at bmb.sdu.dk>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("PolySTest")

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("PolySTest")
PolySTest HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, MassSpectrometry, Proteomics, Software
Version 0.99.6
In Bioconductor since BioC 3.20 (R-4.4)
License GPL-2
Depends R (>= 4.4.0)
Imports fdrtool (>= 1.2.15), limma(>= 3.44.3), matrixStats (>= 0.57.0), qvalue(>= 2.22.0), shiny (>= 1.5.0), SummarizedExperiment(>= 1.20.0), knitr (>= 1.33), plotly (>= 4.9.4), heatmaply (>= 1.1.1), circlize (>= 0.4.12), UpSetR (>= 1.4.0), gplots (>= 3.1.1), S4Vectors(>= 0.30.0), parallel (>= 4.1.0), grDevices (>= 4.1.0), graphics (>= 4.1.0), stats (>= 4.1.0), utils (>= 4.1.0)
System Requirements
URL https://github.com/computproteomics/PolySTest
Bug Reports https://github.com/computproteomics/PolySTest/issues
See More
Suggests testthat (>= 3.0.0), BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package PolySTest_0.99.6.tar.gz
Windows Binary PolySTest_0.99.6.zip (64-bit only)
macOS Binary (x86_64) PolySTest_0.99.6.tgz
macOS Binary (arm64) PolySTest_0.99.6.tgz
Source Repository git clone https://git.bioconductor.org/packages/PolySTest
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PolySTest
Bioc Package Browser https://code.bioconductor.org/browse/PolySTest/
Package Short Url https://bioconductor.org/packages/PolySTest/
Package Downloads Report Download Stats