DEprot

R package to impute, normalize and perform differential analyses on proteomics data (LFQ-based)

Introduction

The concept behind DEprot (Differential Expression proteomics) is to provide a toolkit that allows for the normalization, imputation and analyses of the differential protein expression in proteomics data. The data are assumed to be LFQ (label-free quantitation) values.

Citation

If you use this package, please cite:

*No publication associated yet.*

Installation

Developmental versions

## Install remotes from CRAN (if not already installed)
if (!require("remotes", quietly = TRUE)) {
  install.packages("remotes")
}

# Install the DEprot package
remotes::install_github("sebastian-gregoricchio/DEprot",
                        build_manual = TRUE,
                        build_vignettes = TRUE)

Possibile installation issues

External dependencies

The package aPEAR (Kerseviciute & Gordevicius, Bioinformatics 2023) is required for the ORA/GSEA analyses. However, recently, it is has been removed from the CRAN, but it can be installed using:

remotes::install_github("sebastian-gregoricchio/aPEAR",
                        build_manual = FALSE,
                        build_vignettes = FALSE)

Another package possibly required, is prolfqua:

remotes::install_github("fgcz/prolfqua",
                        build_manual = FALSE,
                        build_vignettes = FALSE)

renv

In order to avoid possible issues, we provide also an renv for the restoration of the packages required for DEprot to work.
We uploaded multiple operative systems and R version builds on the Zenodo repository.
Unzip the build of interest and install the renv package.

## Install renv from CRAN (if not already installed)
install.packages("renv")

## Restore the environment in the DEprot folder
renv::restore(project = "/path/to/DEprot_renv_folder")

## Install DEprot (if not already installed)
if (!require("DEprot", quietly = TRUE)) {
  remotes::install_github("sebastian-gregoricchio/DEprot",
                          build_manual = TRUE,
                          build_vignettes = TRUE)
}

Documentation

With the package a web-manual and a vignette are available. The vignette can be inspected on R as well by typing browseVignettes("DEprot").

Other examples of DEprot usage can be found on Zenodo.

Package history and releases

A list of all releases and respective description of changes applied could be found here.

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Contact

For any suggestion, bug fixing, commentary please report it in the issues/request tab of this repository.

License

This package is under a GNU General Public License (version 3).

Contributors