A collection (read: hodgepodge) of tools for bioinformatics tasks.
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 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
$ pip install python-bioinformagickshttps://python-bioinformagicks.readthedocs.io
This package was created by Sylvia N. Michki.
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
Free software: GNU General Public License v3