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
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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
| Maintainer | Veit Schwämmle <veits@bmb.sdu.dk> |
| Author | Veit Schwämmle [aut, cre] (ORCID: <https://orcid.org/0000-0002-9708-6722>) |
| License | GPL-2 |
| URL | https://github.com/computproteomics/PolySTest |
| Bug Reports | https://github.com/computproteomics/PolySTest/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, MassSpectrometry, Proteomics, Software |
| Package Short Url | https://bioconductor.org/packages/PolySTest/ |
Citation
From within R, enter citation("PolySTest"):
Veit Schwämmle. PolySTest: PolySTest: Detection of differentially regulated features. Combined statistical testing for data with few replicates and missing values. doi:10.18129/B9.bioc.PolySTest, R package version 1.6.0, https://bioconductor.org/packages/PolySTest.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | PolySTest_1.6.0.tar.gz |
| Windows binary (x86_64) | PolySTest_1.6.0.zip |
| macOS binary (arm64) | PolySTest_1.6.0.tgz |
| macOS binary (x86_64) | PolySTest_1.6.0.tgz |
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