MSstatsSampleSize

DOI: 10.18129/B9.bioc.MSstatsSampleSize    

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

Bioconductor version: Release (3.10)

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 "3.6") 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 1.0.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License Artistic-2.0
Depends R (>= 3.6)
Imports ggplot2, BiocParallel, caret, gridExtra, reshape2, stats, utils, grDevices, graphics
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_1.0.0.tar.gz
Windows Binary MSstatsSampleSize_1.0.0.zip
Mac OS X 10.11 (El Capitan) MSstatsSampleSize_1.0.0.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

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