Utility functions for scanpy
Project description
Utility functions for scanpy
Free software: MIT license
Installation
pip install scanpy-utils
Documentation
See https://scanpy-utils.readthedocs.io/en/latest/reference/index.html
Development
To run all the tests run:
tox
Note, to combine the coverage data from all the tox environments run:
Windows |
set PYTEST_ADDOPTS=--cov-append tox |
---|---|
Other |
PYTEST_ADDOPTS=--cov-append tox |
Changelog
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
Plotting:
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
Project details
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