SEMITONES identifies highly enriched features in single-cell omics data without prior clustering. For a detailed description of SEMITONES, please check out the manuscript. For analysis scripts and notebooks relating to the manuscript, please consult the manuscript's GitHub page.
You can install the in-development version with:
pip install https://github.com/ohlerlab/SEMITONES/archive/master.zip
Usage examples for the basic SEMITONES functionality are provided by means of Jupyter Notebooks in the tutorial directory.
- Reference cell selection
- Enrichment scoring
- Gene set enrichment scoring
- Enrichment scoring for feature selection
If you have trouble opening the Jupyter Notebooks on GitHub, try accessing them through the Jupyter Notebook viewer
Documentation on individual functions can be found in the project`s wiki.
SEMITONES has been tested on a Linux system running CentOS 7 and developed in and tested for Python 3.6.
To use the figure widget for cell selection in Jupyter Lab or Jupyter Notebooks, please consult the plotly installation instructions.
The package is available under the GPL-v3 license.