MSstatsSampleSize

DOI: 10.18129/B9.bioc.MSstatsSampleSize    

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

Bioconductor version: Release (3.11)

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>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("MSstatsSampleSize")

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("MSstatsSampleSize")

 

HTML	R Script	MSstatsSampleSize User Guide
PDF		Reference Manual

Details

biocViews	Classification, DifferentialExpression, ExperimentalDesign, MassSpectrometry, PrincipalComponent, Proteomics, Software, Visualization
Version	1.2.0
In Bioconductor since	BioC 3.10 (R-3.6) (1 year)
License	Artistic-2.0
Depends	R (>= 3.6)
Imports	ggplot2, BiocParallel, caret, gridExtra, reshape2, stats, utils, grDevices, graphics, MSstats
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	http://msstats.org
BugReports	https://groups.google.com/forum/#!forum/msstats
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MSstatsSampleSize_1.2.0.tar.gz
Windows Binary	MSstatsSampleSize_1.2.0.zip
macOS 10.13 (High Sierra)	MSstatsSampleSize_1.2.0.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
Old Source Packages for BioC 3.11	Source Archive