Skip to main content

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

0.1.1 (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

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

scanpy-utils-0.1.1.tar.gz (16.9 kB view hashes)

Uploaded source

Built Distribution

scanpy_utils-0.1.1-py2.py3-none-any.whl (7.9 kB view hashes)

Uploaded py2 py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page