This repository contains utilities used in the analysis of the Murine Aging Cell Atlas.

• aging_vec.py contains functions to compute vectors of difference within an embedding between two groups of cells.
• cell_subtype_heirarchy.py formalizes our notions of cell states within each cell type and defines lists of marker genes gathered from the Tabula Muris.
• diffex.py contains tools for differential expression.
• ot_distances.py implements a discrete optimal transport distance calculation which we used to compare young and old cell types.
• scanpy_fxn.py contains assorted functions for quality control and clustering.
• variation.py contains functions for computing metrics of gene expression variance and cell-cell heterogeneity.