python-bioinformagicks 0.4.2

A collection of tools for various bioinformatics tasks.

A collection (read: hodgepodge) of tools for bioinformatics tasks.

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

• Basic single-cell variant calling for single point mutations

Plotting:

• Split embedding plot generation based on categorical observations

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

• Barplot generation for gProfiler ORA results, with optional term fold enrichment sorting

Utilities:

• Identification of genes often left ignored, like AW146154

• Combination of categorical columns maintaining specified ordering

Installation

$ pip install python-bioinformagicks

Documentation

https://python-bioinformagicks.readthedocs.io

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