Extract hierarchical signatures of cell state from single-cell data.
Project description
Deep exponential families for single-cell data. scDEF learns de novo gene signatures from scRNA-seq data at multiple levels of resolution.
Installation
pip install scdef
Please be sure to install a version of JAX that is compatible with your GPU (if applicable).
Getting started
scDEF takes as input an AnnData object containing filtered, but not normalized, UMI counts. The notebooks directory contains IPython notebooks with examples showcasing the analyses enabled by scDEF.
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