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Tools associated with the Calico Murine Aging Cell Atlas, Kimmel 2019 et. al., Genome Research

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Murine aging cell atlas

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

Table of Contents

  • 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.

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Tools associated with the Calico Murine Aging Cell Atlas, Kimmel 2019 et. al., Genome Research

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