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MSstatsSampleSize

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.18 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see MSstatsSampleSize.

Simulation tool for optimal design of high-dimensional MS-based proteomics experiment


Bioconductor version: Release (3.18)

The packages estimates the variance in the input protein abundance data and simulates data with predefined number of biological replicates based on the variance estimation. It reports the mean predictive accuracy of the classifier and mean protein importance over multiple iterations of the simulation.

Author: Ting Huang [aut, cre], Meena Choi [aut], Olga Vitek [aut]

Maintainer: Ting Huang <thuang0703 at gmail.com>

Citation (from within R, enter citation("MSstatsSampleSize")):

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("MSstatsSampleSize")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews Classification, DifferentialExpression, ExperimentalDesign, MassSpectrometry, PrincipalComponent, Proteomics, Software, Visualization
Version 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License Artistic-2.0
Depends R (>= 3.6)
Imports ggplot2, BiocParallel, caret, gridExtra, reshape2, stats, utils, grDevices, graphics, MSstats
System Requirements
URL http://msstats.org
Bug Reports https://groups.google.com/forum/#!forum/msstats
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Suggests BiocStyle, knitr, rmarkdown, testthat
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Package Archives

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

Source Package
Windows Binary MSstatsSampleSize_1.16.0.zip
macOS Binary (x86_64) MSstatsSampleSize_1.16.0.tgz
macOS Binary (arm64) MSstatsSampleSize_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MSstatsSampleSize
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MSstatsSampleSize
Package Short Url https://bioconductor.org/packages/MSstatsSampleSize/
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