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Utility functions for scanpy

Project description

Utility functions for scanpy

  • Free software: MIT license


pip install scanpy-utils


To run all the tests run:


Note, to combine the coverage data from all the tox environments run:

set PYTEST_ADDOPTS=--cov-append
PYTEST_ADDOPTS=--cov-append tox


0.1.1 (2021-08-11)

  • Fix get_markers function to add pct.1 and pct.2 columns even if no markers were found.

0.1 (2021-06-24) Initial release

  • get_markers function to extract markers from adata and add pct.1, pct.2 fields
  • write_mtx function to dump adata in cellranger mtx format
  • clean_metadata function to merge and remove duplicates from adata.var after merging


  • feature_plot function to plot hexbin feature plot on UMAP
  • plot_composition function to plot composition of clusters based on other metadata
  • expr_colormap function with custom colormap for expression

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