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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, MassSpectrometry, Proteomics, Software |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 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
| 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_1.7.0.tar.gz |
| Windows Binary (x86_64) | PolySTest_1.7.0.zip |
| macOS Binary (big-sur-x86_64) | PolySTest_1.7.0.tgz |
| macOS Binary (sonoma-arm64) | PolySTest_1.7.0.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 |