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General

  • Installation
  • API
    • pydeseq2.dds.DeseqDataSet
    • pydeseq2.ds.DeseqStats
    • pydeseq2.inference.Inference
    • pydeseq2.default_inference.DefaultInference
    • pydeseq2.datasets
    • pydeseq2.dispersions
    • pydeseq2.distributions
    • pydeseq2.glm
    • pydeseq2.grid_search
    • pydeseq2.misc
    • pydeseq2.plotting
    • pydeseq2.preprocessing
    • pydeseq2.stats
  • Contributing
  • References

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  • Getting Started
    • Loading data and saving results with pandas and pickle
    • Step-by-step PyDESeq2 workflow
    • A simple PyDESeq2 workflow

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Getting Started

Getting Started#

Loading data and saving results with pandas and pickle

Loading data and saving results with pandas and pickle

Step-by-step PyDESeq2 workflow

Step-by-step PyDESeq2 workflow

A simple PyDESeq2 workflow

A simple PyDESeq2 workflow

Download all examples in Python source code: auto_examples_python.zip

Download all examples in Jupyter notebooks: auto_examples_jupyter.zip

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References

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Loading data and saving results with pandas and pickle

© Copyright 2026, Boris Muzellec, Maria Telenczuk, Vincent Cabelli, Mathieu Andreux.