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.
Using MUFFIN
examples/3k_pbmc_clustering.ipynb examples/scATAC_clustering.ipynb examples/H3K4Me3_chip_immune.ipynb examples/ATAC_TCGA.ipynb examples/10k_pbmc_clustering.ipynb
muffin