npyc
The nPYc-Toolbox defines objects for representing, and implements functions to manipulate and display, metabolic profiling datasets.
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
4 of 10 committers (40.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.8%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
The nPYc-Toolbox defines objects for representing, and implements functions to manipulate and display, metabolic profiling datasets.
Basic Info
- Host: GitHub
- Owner: phenomecentre
- License: mit
- Language: Python
- Default Branch: master
- Size: 5.51 MB
Statistics
- Stars: 25
- Watchers: 7
- Forks: 8
- Open Issues: 41
- Releases: 6
Topics
Metadata Files
README.md
nPYc Toolbox 
A Python implementation of the NPC toolchain for the import, quality-control, and preprocessing of metabolic profiling datasets.
Imports:
- Peak-picked LC-MS data (XCMS, Progenesis QI, & Metaboscape)
- Raw NMR spectra (Bruker format)
- Targeted datasets (TargetLynx, Bruker BI-LISA & BI-Quant-Ur)
Provides:
- Batch & drift correction for LC-MS datasets
- Feature filtering by RSD and linearity of response
- Calculation of spectral line-width in NMR
- PCA of datasets
- Visualisation of datasets
Exports:
- Basic tabular csv
- ISA-TAB
Tutorials:
- Available at nPYc-toolbox-tutorials, see below.
Installation
For full installation instructions see Installing the nPYc-Toolbox
To install via pip, run:
pip install nPYc
To install from a local copy of the source, simply navigate to the main package folder and run:
python setup.py install
Alternatively, using pip and a local copy of the source:
pip install /nPYC-toolboxDirectory/
To update the current installed version use:
pip install --upgrade nPYc
Installation with pip allows the usage of the uninstall command
pip uninstall nPYc
Documentation
Documentation is hosted on Read the Docs.
Documentation is generated via Sphinx Autodoc, documentation markup is in reStructuredText.
To build the documentation locally, cd into the docs directory and run:
make html
To clear the current documentation in order to rebuild after making changes, run:
make clean
Tutorials
A repository containing exemplar datasets and Jupyter notebook tutorials to demonstrate the application of the nPYc-Toolbox for the preprocessing and quality control of LC-MS, NMR and targeted NMR (Bruker IVDr) metabolic profiling data is available for download from nPYc-toolbox-tutorials.
For new users, we strongly recommend downloading these tutorials, which provide detailed worked examples with links to relevant documentation.
Development
Source management is git-flow-like - no development in the master branch! When making a change, create a fork based on develop, and issue a pull request when ready.
When merging into the develop branch, all new code must include unit-tests, all tests should pass, and overall code-coverage for the toolbox should not drop.
Releases
When merging from develop (or hotfix branches) into release, ensure:
- All references to the debugger are removed
- All paths are relative and platform agnostic
- All tests pass
Testing
Unit testing is managed via the unittest framework. Test coverage can be found on codecov.io.
To run all tests, cd into the Tests directory and run:
python -m unittest discover -v
Individual test modules can be run with:
python -m `test_filename` -v
Owner
- Name: National Phenome Centre
- Login: phenomecentre
- Kind: organization
- Website: http://phenomecentre.org
- Repositories: 4
- Profile: https://github.com/phenomecentre
GitHub Events
Total
- Issues event: 1
- Watch event: 1
- Member event: 2
- Issue comment event: 1
- Push event: 6
Last Year
- Issues event: 1
- Watch event: 1
- Member event: 2
- Issue comment event: 1
- Push event: 6
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| gscorreia89 | g****9@g****m | 220 |
| Caroline Sands | c****1@i****k | 66 |
| Jake TM Pearce | j****t@g****m | 65 |
| Gordon Haggart | g****3@g****m | 13 |
| Jazz Mack Smith | j****h@i****k | 10 |
| Jazz Mack Smith | j****3@i****k | 4 |
| adwolfer | a****2@i****k | 1 |
| Arnaud M. Wolfer | a****r@g****m | 1 |
| Noureddin Sadawi | n****i@g****m | 1 |
| misch91 | 9****1 | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 65
- Total pull requests: 42
- Average time to close issues: 8 months
- Average time to close pull requests: about 1 month
- Total issue authors: 9
- Total pull request authors: 8
- Average comments per issue: 1.03
- Average comments per pull request: 0.9
- Merged pull requests: 33
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Gscorreia89 (26)
- jaketmp (15)
- carolinesands (9)
- gordondavies (8)
- misch91 (3)
- Johostman (1)
- lauzikaite (1)
- kopeckylukas (1)
- RicardoMBorges (1)
Pull Request Authors
- Gscorreia89 (18)
- gordondavies (8)
- jaketmp (6)
- carolinesands (4)
- nsadawi (3)
- lauzikaite (1)
- misch91 (1)
- duibuqi (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 275 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 14
- Total maintainers: 3
pypi.org: npyc
National Phenome Centre toolbox
- Homepage: https://github.com/phenomecentre/npyc-toolbox
- Documentation: https://npyc.readthedocs.io/
- License: MIT
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Latest release: 1.2.8
published almost 3 years ago
Rankings
Maintainers (3)
Dependencies
- Jinja2 *
- cycler *
- iPython *
- isaExplorer *
- isatools *
- lmfit *
- matplotlib *
- networkx *
- numpy *
- pandas *
- plotly *
- pyChemometrics *
- scikit-learn *
- scipy *
- seaborn *
- setuptools *
- statsmodels *
- Jinja2 >=2.10
- cycler >=0.10.0
- iPython >=6.3.1
- isaExplorer >=0.1
- isatools >=0.9.3
- lmfit >=0.9.7
- matplotlib >=2.2.2
- networkx >=2.1
- numpy >=1.14.2
- pandas >=0.23.0
- plotly >=3.1.0
- pyChemometrics >=0.1
- scikit-learn >=0.19.1
- scipy >=1.1.0
- seaborn >=0.8.1
- setuptools >=39.1.0
- statsmodels >=0.9.0
- actions/checkout v2 composite
- actions/setup-python v2 composite
- pypa/gh-action-pypi-publish master composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- codecov/codecov-action v1 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- codecov/codecov-action v1 composite