Rsripts_for_proteomics

About

Scripts for parsing the output of proteomics analyses.

Functions to do the following:

1. Parse the mzTab output from quantms
2. Parse the msstats_input file from quantms
3. Parse the diann parquet output
4. Prepare dataframes for EDA and differential analysis with prolfqua

Can add Rmd files or links to other projects later to show example usage.

Installation

# if devtools not installed
# install.packages("devtools")

library(devtools)
devtools::install_github("Roman-Si/Rsripts_for_proteomics")

Usage

An analysis using this package can be found in https://github.com/Roman-Si/Asp-parasiticus_alkane_multiomics

Template projects

Proteomics R packages used:

• prolfqua
• MsnBase

Pipelines used for analysis of LC-MS/MS data:

• quantms for DDA
• DIA-NN for DIA

Ideas for packaging taken from

• Building reproducible analytical pipelines with R, https://raps-with-r.dev/
• Reproducible and Trustworthy Workflows for Data Science, https://ubc-dsci.github.io/reproducible-and-trustworthy-workflows-for-data-science/