python-bioinformagicks 0.3.0

A collection of tools for various bioinformatics tasks.

A collection of tools for various bioinformatics tasks.

Documentation

https://python-bioinformagicks.readthedocs.io

Features

Tools:

• TF-IDF marker gene testing (“quickMarkers”), as in SoupX

• JASMINE gene set scoring, as in Noureen et al.

• Over-representation analyses (ORAs) with gProfiler

• Cell mask generation based on geometric sketching, as in Geosketch

• Cell mask generation based on embedding (i.e. UMAP) coordinate bounds

• Z-standard scaling of gene expression on a per-group basis

Plotting:

• Split embedding plots based on categorical observations

• Stacked barplot generation of cell proportions split by group and counts normalized per-batch

Utilities:

• Identification of genes often left ignored, like AW146154

• Combination of categorical columns maintaining specified ordering

Credits

This package was created by Sylvia N. Michki.

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

License

Free software: GNU General Public License v3