ProteomicsUtils

A collection of utility functions for processing, analysing and plotting proteomic data

Please note: These functions alone do not constitute a complete analysis pipeline, and instead are meant for use in conjunction with additional packages (forthcoming in future releases). In addition, these functions require the preprocessing of raw MS datafiles with an identification and quantification program such as MaxQuant or ProteomeDiscoverer.

Prerequisites

This package assumes the standard installation of Python3. For specific package requirements, see the requirements.txt file.

Authors

Dezerae Cox - Initial work - dezeraecox

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

Templates for this package were adapted from PurpleBooth
Kudos to the 2018 Asia-Pacific Advanced Scientific Programming in Python (#ASPP) Summer School for giving me the condfidence and tools to tackle my first python package!

Module Dev Checklist

Standard Utility Modules

Specific MS analysis Modules

Peptide abundance histogram

  PeptideAbundanceHistogram.main(input_path, output_path, sample_name)

Volcano plot of protein abundance changes

  AbundanceVolcanoPlot.main(input_path, output_path, sample_name)

Foldedness scatterplot from peptides
Heatmap of comparison between stress treatments
Cluster analysis according to GO thermofisher
Gene mapping functionality for UniProtKB accessions

dezeraecox/ProteomicsUtils