metabolinks
A set of tools for high-resolution MS metabolomics data analysis
Science Score: 67.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.6%) to scientific vocabulary
Last synced: 6 months ago
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Repository
A set of tools for high-resolution MS metabolomics data analysis
Basic Info
- Host: GitHub
- Owner: aeferreira
- License: mit
- Language: Python
- Default Branch: master
- Size: 1.36 MB
Statistics
- Stars: 2
- Watchers: 3
- Forks: 3
- Open Issues: 1
- Releases: 1
Created over 8 years ago
· Last pushed over 2 years ago
Metadata Files
Readme
License
Citation
Authors
README.rst
***********
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`` 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).
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5336951.svg
:target: https://doi.org/10.5281/zenodo.5336951
Installing
==========
``Metabolinks`` is distributed on PyPI_ and can be installed with pip on
a Python 3.6+ installation::
pip install metabolinks
.. _PyPI: https://pypi.org/project/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
Owner
- Name: António E. N. Ferreira
- Login: aeferreira
- Kind: user
- Location: Lisbon, Portugal
- Repositories: 3
- Profile: https://github.com/aeferreira
Citation (CITATION.cff)
cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: metabolinks
abstract: a Python package for high-resolution-MS metabolomics data analysis.
authors:
- given-names: António
family-names: Ferreira
name-particle: E.N.
affiliation: University of Lisbon, Portugal
orcid: "https://orcid.org/0000-0002-9625-8115"
- given-names: Francisco
family-names: Traquete
affiliation: University of Lisbon, Portugal
orcid: "https://orcid.org/0000-0002-4081-6544"
version: 0.71
date-released: "2021-08-30"
identifiers:
- description: This is the collection of archived snapshots of all versions of Metabolinks
type: doi
value: "10.5281/zenodo.5336950"
- description: This is the archived snapshot of version 0.71 of Metabolinks
type: doi
value: "10.5281/zenodo.5336951"
repository-code: "https://github.com/aeferreira/metabolinks"
license: MIT
GitHub Events
Total
Last Year
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| aeferreira | f****e@g****m | 164 |
| RuiNascimento | r****3@h****m | 12 |
| Beatriz Lima | b****l@h****m | 4 |
| gilpires97 | g****7@g****m | 3 |
| Beatriz Lima | 4****a | 3 |
| Francisco-T | f****t@g****m | 2 |
| aeferreira | a****a | 1 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 0
- Total pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: about 1 month
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- beatriz-lima (3)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 28 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 5
- Total maintainers: 1
pypi.org: metabolinks
A set of tools for high-resolution MS metabolomics data analysis
- Homepage: https://github.com/aeferreira/metabolinks
- Documentation: https://metabolinks.readthedocs.io/
- License: MIT
-
Latest release: 1.0.0
published over 4 years ago
Rankings
Dependent packages count: 10.0%
Forks count: 16.8%
Dependent repos count: 21.7%
Average: 30.0%
Stargazers count: 31.9%
Downloads: 69.5%
Maintainers (1)
Last synced:
6 months ago
Dependencies
binder/environment.yml
pypi
pyproject.toml
pypi
- matplotlib >=2.0
- numpy *
- pandas >=0.25
- pandas-flavor *
- requests *
- scikit-learn >=1.0
- scipy *
- xlrd *
- xlsxwriter *