PhenoFeatureFinder
PhenoFeatureFinder: a python package for linking developmental phenotypes to omics features - Published in JOSS (2024)
Science Score: 95.0%
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Published in Journal of Open Source Software
Scientific Fields
Repository
A Python package dedicated to identifying plant metabolite features related to insect resistance
Basic Info
Statistics
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
- Releases: 2
Metadata Files
README.md
PhenoFeatureFinder
Linking developmental phenotypes to metabolic features
PhenoFeatureFinder is divided into three classes:
* PhenotypeAnalysis
* OmicsAnalysis
* FeatureSelection
PhenotypeAnalysis was designed to analyse development over time through progressive stages in multiple groups or treatments. This could for example be the development of insects through their larval stages over time in different environments, or disease scores of fungal infections in multiple host plants. These types of phenotyping analyses can be challenging, due to the many variables involved (e.g. time, developmental stages, replicates, treatments), especially for researchers whose strength does not lie in data analysis. PhenotypeAnalysis offers a set of functions to visualise the development while taking into account those different variables, and to perform the necessary data preprocessing steps. From the output, it is easy to manually assign binary phenotypes to your groups (treatments, genotypes, etc), if you want to use it as input for FeatureSelection.
With OmicsAnalysis, you can filter large untargeted metabolomics datasets and visualise the structure of the data. The filtered data and a corresponding set of binary phenotypes can then be used as input for FeatureSelection. With only a few lines of code, the best fitting pipeline to link the phenotypes to metabolic features is created using Automated Machine Learning with TPOT and scikit-learn.
Although OmicsAnalysis and FeatureSelection are designed for metabolomics data, they might also be used for other types of omics data. The user would have to keep in mind that the functions were written for the specifics of metabolomics data (high sparsity, strongly correlated features) and first assess the fit for other types of data.
Installation
bash
$ pip install PhenoFeatureFinder
At this moment, PhenoFeatureFinder requires python 3.9.
Usage
For each of the classes, you can find a manual with an explanation for all of their functions in the manuals folder. Alternatively, you can find the documentation of the classes and their functions on Read the Docs.
If you want to see an example of how PhenoFeatureFinder can be used for real-world data, you can take a look at one of the two examples. The first example showcases the use of the PhenotypeAnalysis class for the analysis of the development of caddisfly larvae in four freshwater streams. In the second example, the OmicsAnalysis and FeatureSelection classes are used to analyse and select interesting features from a mass spectrometry dataset of a panel of bacterial species.
Dependencies
Required for all classes: - NumPy - pandas - Matplotlib - seaborn
Additionally required for PhenotypeAnalysis: - SciPy
Additionally required for OmicsAnalysis: - scikit-learn - UpSetPlot
Additionally required for FeatureSelection: - scikit-learn - TPOT - auto-sklearn (auto-sklearn is made for Linux operating systems. On macOS it needs to be installed manually with brew and pip. You can do this by following these instructions.)
Testing
Before using PhenoFeatureFinder to analyse your data, follow the manuals using the accompanying data to test the functionality. The obtained results should be identical to those in the manual. If you run into any errors, please contact the authors.
Citation
Insert citation option when ready
Contributing
Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.
Author contributions
PhenoFeatureFinder was created by Lissy-Anne Denkers and Marc Galland, with input from Annabel Dekker, Valerio Bianchi and Petra Bleeker.
License
This package is licensed under the terms of the Apache License 2.0 license.
Credits
PhenoFeatureFinder was created with cookiecutter and the py-pkgs-cookiecutter template.
Useful reading
Owner
- Name: Petra Bleeker laboratory
- Login: BleekerLab
- Kind: organization
- Email: P.M.Bleeker@uva.nl
- Location: University of Amsterdam
- Repositories: 6
- Profile: https://github.com/BleekerLab
Laboratory of Petra Bleeker at University of Amsterdam
JOSS Publication
PhenoFeatureFinder: a python package for linking developmental phenotypes to omics features
Authors
University of Amsterdam, Department of Plant Physiology, Green Life Science Research Theme, Swammerdam Institute for Life Sciences, Amsterdam, The Netherlands
INRAE, Institute of Genetics, Environment and Plant Protection (IGEPP—Joint Research Unit 1349), Le Rheu, France
Enza Zaden R&D B.V., BTR-BM Bioinformatics, Enkhuizen, The Netherlands
Enza Zaden R&D B.V., BTR-BM Bioinformatics, Enkhuizen, The Netherlands, Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, Netherlands
University of Amsterdam, Department of Plant Physiology, Green Life Science Research Theme, Swammerdam Institute for Life Sciences, Amsterdam, The Netherlands
Editor
Julia Romanowska
Tags
insect development phenotyping metabolomics omics feature selection preprocessingGitHub Events
Total
- Release event: 1
- Push event: 10
Last Year
- Release event: 1
- Push event: 10
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| LissyDenkers | l****s@u****l | 141 |
| Marc Galland | m****d@u****l | 32 |
| Lissy Denkers | l****s@f****l | 9 |
| Petra Bleeker | 5****r | 1 |
| semantic-release | s****e | 1 |
| Lissy Denkers | l****s@w****l | 1 |
Committer Domains (Top 20 + Academic)
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Last synced: 4 months ago
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Packages
- Total packages: 1
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Total downloads:
- pypi 14 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 2
pypi.org: phenofeaturefinder
Find metabolic features linked to insect development phenotypes
- Homepage: https://github.com/BleekerLab/PhenoFeatureFinder
- Documentation: https://phenofeaturefinder.readthedocs.io/
- License: Apache-2.0
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Latest release: 0.1.4
published about 1 year ago
Rankings
Maintainers (2)
Dependencies
- actions/checkout v4 composite
- actions/upload-artifact v1 composite
- openjournals/openjournals-draft-action master composite
- alabaster ==0.7.16
- cookiecutter >=2.6.0
- myst-nb *
- pytest ==8.1.1
- pytest-cookies ==0.7.0
- ruff ==0.3.5
- sphinx-autoapi *
- sphinx-rtd-theme *
- tox ==4.14.2
- watchdog ==4.0.0
- 136 dependencies
- myst-nb 0.17.1 develop
- pytest >=7.2.0 develop
- python-semantic-release >=7.32.2 develop
- sphinx-autoapi >=2.0.0 develop
- sphinx-markdown-tables >=0.0.17 develop
- sphinx-rtd-theme >=1.1.1 develop
- TPOT >=0.11.7
- matplotlib >=3.4.3
- numpy 1.25.0
- pandas >=1.5.1
- python 3.9
- scikit-learn >=0.24.1
- scipy >=1.10.1
- seaborn >=0.12.1
- upsetplot >=0.8.0