metabolinks 1.0.0

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

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

• common metabolomics data-matrix preprocessing, based on pandas and scikit-learn

• 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).

Installing

Metabolinks is distributed on PyPI and can be installed with pip on a Python 3.6+ 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:

• Anaconda (or Miniconda followed by the necessary conda install’s)

• Enthought Canopy

The formal requirements are:

• Python 3.6 and above

• setuptools, pip, requests, pandas-flavor and pytest

From the Python scientific ecossystem:

• numpy, scipy, matplotlib, pandas and scikit-learn

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