tidyms 0.7.0

Tools for working with MS data in metabolomics

TidyMS: Tools for working with MS data in metabolomics

TidyMS is a python library for processing Mass Spectrometry data. It aims to provide easy to use tools to read, process and visualize MS data generated in metabolomic studies.

Features

TidyMS provides functionality to:

1. Read raw MS data in the mzML format
2. Spectrum and chromatogram creation.
3. Powerful and flexible peak picking functions optimized for chromatographic and spectral data.
4. Feature detection and feature correspondence in LC-MS data.
5. Reading processed data in a variety of formats (XCMS, MZMine2, ...)
6. Data matrix curation using widely accepted guidelines from the metabolomics community.
7. Interactive visualizations of raw and processed data using Bokeh, or publication quality plots using seaborn.

Installation

The latest release can be installed from PyPI:

    pip install tidyms

Examples

Jupyter notebooks with examples are available here.

Tests

TidyMS uses unit tests for most of its functionality. The tests can be executed with

    python setup.py test

Documentation

The official documentation is available at readthedocs.

Citation

If you find TidyMS useful, we would appreciate citations:

Riquelme, G.; Zabalegui, N.; Marchi, P.; Jones, C.M.; Monge, M.E. A Python-Based Pipeline for Preprocessing LC–MS Data for Untargeted Metabolomics Workflows. Metabolites 2020, 10, 416, doi:10.3390/metabo10100416.