ProteoMM

DOI: 10.18129/B9.bioc.ProteoMM    

This is the development version of ProteoMM; for the stable release version, see ProteoMM.

Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform

Bioconductor version: Development (3.9)

ProteoMM is a statistical method to perform model-based peptide-level differential expression analysis of single or multiple datasets. For multiple datasets ProteoMM produces a single fold change and p-value for each protein across multiple datasets. ProteoMM provides functionality for normalization, missing value imputation and differential expression. Model-based peptide-level imputation and differential expression analysis component of package follows the analysis described in “A statistical framework for protein quantitation in bottom-up MS based proteomics" (Karpievitch et al. Bioinformatics 2009). EigenMS normalisation is implemented as described in "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition." (Karpievitch et al. Bioinformatics 2009).

Author: Yuliya V Karpievitch, Tim Stuart and Sufyaan Mohamed

Maintainer: Yuliya V Karpievitch <yuliya.k at gmail.com>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ProteoMM", version = "3.9")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ProteoMM")

 

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Details

biocViews DifferentialExpression, MassSpectrometry, Normalization, Proteomics, Software
Version 1.1.0
License MIT
Depends R (>= 3.5)
Imports gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats, graphics
LinkingTo
Suggests BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report  

Package Archives

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

Source Package ProteoMM_1.1.0.tar.gz
Windows Binary ProteoMM_1.1.0.zip
Mac OS X 10.11 (El Capitan) ProteoMM_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ProteoMM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ProteoMM
Package Short Url http://bioconductor.org/packages/ProteoMM/
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