PolySTest
This is the released version of PolySTest; for the devel version, see PolySTest.
PolySTest: Detection of differentially regulated features. Combined statistical testing for data with few replicates and missing values
Bioconductor version: Release (3.21)
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("PolySTest")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, MassSpectrometry, Proteomics, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (1 year) |
| 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
| 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_1.2.0.tar.gz |
| Windows Binary (x86_64) | PolySTest_1.2.0.zip (64-bit only) |
| macOS Binary (x86_64) | PolySTest_1.2.0.tgz |
| macOS Binary (arm64) | PolySTest_1.2.0.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 |