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A set of metabolomics tools for use in Galaxy
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README.md

README.md

Synopsis

SECIMTools project aims to develop a suite of tools for processing of metabolomics data, which can be run in a standalone mode or via Galaxy Genomics Framework.

Motivation

The SECIMTools a set of python tools that are available both as standalone and wrapped for use in Galaxy. The suite includes a comprehensive set of quality control metrics (retention time window evaluation and various peak evaluation tools), visualization techniques (hierarchical cluster heatmap, principal component analysis, linear discriminant analysis, modular modularity clustering), basic statistical analysis methods (partial least squares - discriminant analysis, analysis of variance), advanced classification methods (random forest, support vector machines), and advanced variable selection tools (least absolute shrinkage and selection operator LASSO and Elastic Net).

Installation

SECIMTools are available as a secimtools pypi package. Project has also been packaged for bioconda and Galaxy Genomics Framework.

Contributors

Feel free to fork the repository and submit pull requests.

License

The project is licensed under MIT license

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