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

DOI: 10.18129/B9.bioc.MSstatsSampleSize

Bioconductor version: 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

Need some help? Ask on the Bioconductor Support site!

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

Suggests BiocStyle, knitr, rmarkdown, testthat

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

Windows Binary MSstatsSampleSize_1.16.0.zip (64-bit only)

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/

Package Downloads Report Download Stats