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Bioconductor - PolySTest (development version)

PolySTest

This is the development version of PolySTest; for the stable release version, see PolySTest.

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

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-9708-6722

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

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

To install this package, start R (version "4.5") 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")
Details biocViews DifferentialExpression, MassSpectrometry, Proteomics, Software Version 1.3.1 In Bioconductor since BioC 3.20 (R-4.4) (0.5 years) License GPL-2 Depends R (>= 4.4.0) Imports fdrtool (>= 1.2.15), limma(>= 3.61.3), 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 Package Archives

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

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