scanpy-utils 0.1.1

Utility functions for scanpy

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

0.1.1 (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

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