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A set of tools for high-resolution MS metabolomics data analysis

Project description

Metabolinks is a Python package that provides a set of tools for high-resolution MS metabolomics data analysis.

Metabolinks aims at providing several tools that streamline most of the metabolomics workflow. These tools were written having ultra-high resolution MS based metabolomics in mind.

Features are a bit scarce right now:

  • peak list alignment
  • data matrix filtering, conversion and sample similarity measures
  • compound taxonomy retrieval

But our road map is clear and we expect to stabilize in a beta version pretty soon.

Stay tuned, and check out the examples folder (examples are provided as jupyter notebooks).


Metabolinks is distributed on PyPI and can be installed with pip on a Python 3.4+ installation:

pip install metabolinks

However, even if Metabolinks is written in Python, it requires some of the powerful scientific packages that are pre-installed on “Scientific/Data Science Python” distributions.

One of these two products is highly recommended:

The formal requirements are:

  • Python 3.4 and above (it runs on Python 2.7 too)
  • setuptools, pip, six, requests and pytest
  • numpy, matplotlib and pandas

The installation of the Jupyter platform is also recommended since the examples are provided as Jupyter notebooks.

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