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PolySTest

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

Bioconductor version: 3.23 · Package version: 1.6.0

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.

Installation

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

BiocManager::install("PolySTest")

Details

MaintainerVeit Schwämmle <veits@bmb.sdu.dk>
AuthorVeit Schwämmle [aut, cre] (ORCID: <https://orcid.org/0000-0002-9708-6722>)
LicenseGPL-2
URLhttps://github.com/computproteomics/PolySTest
Bug Reportshttps://github.com/computproteomics/PolySTest/issues
Downloads rank164
Source branchRELEASE_3_23
biocViewsDifferentialExpression, MassSpectrometry, Proteomics, Software

Documentation

Download

Dependencies

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)

Suggests: testthat (>= 3.0.0), BiocStyle