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Welcome to MUFFIN’s documentation!

MUFFIN is a python package that offers multiple tools for the analysis of count-based functional genomic data. Its flexible count-modelling approach allows to analyze a wide variety of assays of different sizes and sequencing depths, from the bulk to single-cell level. It also includes tools to link genomic regions to genes and functional annotations. Finally, MUFFIN integrates seamlessly into the Scanpy ecosystem.