scanpy-utils

Utility functions for scanpy

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Project description

Utility functions for scanpy

pip install scanpy-utils

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

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

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

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This version

0.1.1

Aug 11, 2021

0.1

Jun 25, 2021

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Uploaded Aug 11, 2021 Source

Uploaded Aug 11, 2021 Python 2 Python 3

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