MSstatsSampleSize
Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
Bioconductor version: Release (3.17)
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("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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MSstatsSampleSize")| MSstatsSampleSize User Guide | HTML | R Script |
| Reference Manual |
Details
| biocViews | Classification, DifferentialExpression, ExperimentalDesign, MassSpectrometry, PrincipalComponent, Proteomics, Software, Visualization |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.6) |
| Imports | ggplot2, BiocParallel, caret, gridExtra, reshape2, stats, utils, grDevices, graphics, MSstats |
| Linking To | |
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| System Requirements | |
| Enhances | |
| URL | http://msstats.org |
| Bug Reports | https://groups.google.com/forum/#!forum/msstats |
See More
| 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_1.13.0.tar.gz |
| Windows Binary | MSstatsSampleSize_1.13.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | MSstatsSampleSize_1.13.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSstatsSampleSize |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSstatsSampleSize |
| Bioc Package Browser | https://code.bioconductor.org/browse/MSstatsSampleSize/ |
| Package Short Url | https://bioconductor.org/packages/MSstatsSampleSize/ |
| Package Downloads Report | Download Stats |