Package: pydeseq2
PyDESeq2 is a python implementation of theDESeq2method [1] for differential expression analysis (DEA) with bulk RNA-seq data, originally in R.
It aims to facilitate DEA experiments for python users.As PyDESeq2 is a re-implementation ofDESeq2from
scratch, you may experience some differences in terms of retrieved values or available features.Currently, available features broadly correspond to the default settings of DESeq2 (v1.34.0) for single-factor and
multi-factor analysis (with categorical or continuous factors) using Wald tests.
We plan to implement more in the future.
In case there is a feature you would particularly like to be implemented, feel free to open an issue.Table of ContentsPyDESeq2Table of ContentsInstallationRequirementsGetting startedDocumentationDataContributing1 - Download the repository2 - Create a conda environmentDevelopment roadmapCiting this workReferencesLicenseInstallationPyPIPyDESeq2can be installed from PyPI usingpip:pip install pydeseq2We recommend installing within a conda environment:conda create -n pydeseq2
conda activate pydeseq2
conda install pip
pip install pydeseq2BiocondaPyDESeq2can also be installed from Bioconda withconda:conda install -c bioconda pydeseq2If you're interested in contributing or want access to the development version, please see thecontributingsection.RequirementsThe list of package version requirements is available insetup.py.For reference, the code is being tested in a github workflow (CI) with python
3.8-3.11 and the following package versions:- anndata 0.8.0
- numpy 1.23.0
- pandas 1.4.3
- scikit-learn 1.1.1
- scipy 1.8.1Please don't hesitate to open an issue in case you encounter any issue due to possible deprecations.Getting startedTheGetting Startedsection of the documentation
contains downloadable examples on how to use PyDESeq2.DocumentationThe documentation is hostedhere on ReadTheDocs.
If you want to have the latest version of the documentation, you can build it from source.
Please go to the dedicatedREADME.mdfor information on how to do so.DataThe quick start examples use synthetic data, provided in this repo (seedatasets.)The experiments described in ourpreprintrely on data
fromThe Cancer Genome Atlas,
which may be obtained from thisportal.ContributingPlease theContributingsection of the
documentation to see how you can contribute to PyDESeq2.1 - Download the repositorygit clone https://github.com/owkin/PyDESeq2.git2 - Create a conda environmentRunconda create -n pydeseq2 python=3.8(or higher python version) to create thepydeseq2environment and then activate it:conda activate pydeseq2.cdto the root of the repo and runpip install -e ."[dev]"to install in developer mode.Then, runpre-commit install.Thepre-committool will automatically runruff,black, andmypy.PyDESeq2 is a living project and any contributions are welcome! Feel free to open new PRs or issues.Development RoadmapHere are some of the features and improvements we plan to implement in the future:Integration to thescverseecosystem:Refactoring to use theAnnDatadata structureSubmitting a PR to be listed as anscverse ecosystempackageVariance-stabilizing transformationImproving multi-factor analysis:Allowing n-level factorsSupport for continuous covariatesImplementing interaction termsCiting this work@article{muzellec2023pydeseq2,
  title={PyDESeq2: a python package for bulk RNA-seq differential expression analysis},
  author={Muzellec, Boris and Telenczuk, Maria and Cabeli, Vincent and Andreux, Mathieu},
  year={2023},
  doi = {10.1093/bioinformatics/btad547},
  journal={Bioinformatics},
}References[1] Love, M. I., Huber, W., & Anders, S. (2014). "Moderated estimation of fold
change and dispersion for RNA-seq data with DESeq2." Genome biology, 15(12), 1-21.https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8[2] Zhu, A., Ibrahim, J. G., & Love, M. I. (2019).
"Heavy-tailed prior distributions for sequence count data:
removing the noise and preserving large differences."
Bioinformatics, 35(12), 2084-2092.https://academic.oup.com/bioinformatics/article/35/12/2084/5159452LicensePyDESeq2 is released under anMIT license.