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Utility functions for scanpy

Project description

Utility functions for scanpy

  • Free software: MIT license

Installation

pip install scanpy-utils

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

Download files

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Files for scanpy-utils, version 0.1.1
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Filename, size scanpy_utils-0.1.1-py2.py3-none-any.whl (7.9 kB) File type Wheel Python version py2.py3 Upload date Hashes View
Filename, size scanpy-utils-0.1.1.tar.gz (16.9 kB) File type Source Python version None Upload date Hashes View

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