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README.md

ProteoModlR

R Suite for Quantitative Proteomics Pathway Modeling.

Overview of pipeline

ProteoModlR is an open-sourced R suite for quantitative mass spectrometry analysis of the relative concentration of proteins and the stoichiometry of post-translational chemical modifications. Due to its modular design and flexible analysis pipeline, ProteoModlR allows for seamless integration with existing proteomics software, such as MaxQuant and Skyline, as well as with statistical and pathway analysis tools. It facilitates analysis and visualization of quantitative proteomics data enabling researchers to assess differential activation of functional cellular processes.

Manifest

QC.R - Script for format verification and data classification

Normalize.R - Script for data normalization

Analyze.R - Script for calculating abundance and stoichiometry

Documentation

Please refer to the PDF file in the vignettes folder

Installation

Enter the following commands directly into R console (assumes devtools is installed):

library(devtools)
install_github('kentsisresearchgroup/ProteoModlR')

Dependencies

'reshape2', 'plyr, and 'ggplot2' from CRAN

Authors

About

R Suite for Quantitative Proteomics Pathway Modeling, as published in Cifani et al BMC Bioinformatics 2017

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