API

dds.DeseqDataSet(*[, adata, counts, ...])	A class to implement dispersion and log fold-change (LFC) estimation.
ds.DeseqStats(dds, contrast[, alpha, ...])	PyDESeq2 statistical tests for differential expression.
inference.Inference()	Abstract class with DESeq2-related inference methods.
default_inference.DefaultInference([...])	Default DESeq2-related inference methods, using scipy/sklearn/numpy.
datasets	Loaders for the example data shipped with PyDESeq2.
dispersions	Estimation of gene-wise and trended dispersions.
distributions	Negative binomial log-likelihoods and their optimization.
glm	Fitting and testing of the negative binomial GLM.
grid_search
misc	Helpers that do not belong to any single step of the pipeline.
plotting	Plots of the fitted model.
preprocessing
stats	Robust summary statistics and smoothing.