Metabolinks
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
andscikit-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, it is recommended to install the the scientific Python packages that are
required by Metabolinks
before using pip
. These are listed below, but they
can be easily obtained by installing one of the "Scientific/Data Science Python" distributions.
One of these two products is highly recommended:
-
Anaconda Individual Edition (or Miniconda followed by the necessary
conda install
's) - Enthought Deployment Manager (followed by the creation of suitable Python environments)
The formal requirements are:
- Python 3.6 and above
-
setuptools
,pip
,requests
,six
,pandas-flavor
andpytest
and, from the Python scientific ecossystem:
-
numpy
,scipy
,matplotlib
,pandas
andscikit-learn
The installation of the Jupyter
platform is also recommended since
the examples are provided as Jupyter notebooks.