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
- 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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