Documentation

MassCube Documentation

Hello! Welcome to the MassCube documentation!

Date: 2025-03-09 Version: 1.2.3

What is MassCube?

MassCube is an open-source computing library and framework for MS data processing in Python. It supports comprehensive functionalities and workflows designed for versatile data processing tasks.

Features

  • Open-source: Free for non-commercial use.

  • Modular design: Easily extendable functionalities.

  • User-friendly: Command-line interface for easy data processing.

  • Scalable: Efficient and memory-friendly handling of large-scale metabolomics data.

  • Reproducible: Metadata tracking for recording parameters, dependencies, and module order.

  • Visualization: Tools for intuitive data exploration and publication-quality figure creation.

Getting Started

Installation Quick Start

Release Notes for v1.2

  • MassCube now annoatate MS/MS spectra using unweighted entropy similarity based on the ms_entropy Python package ver. 1.3.4. Please make sure you use the latest version of the MS/MS library. Check quick start for more details.

  • Now you can plot signal normalization results by setting plot_normalization to True in the parameters.csv file.

  • Bug fixes and performance improvements.