IMPORTANT: This package is very much WIP and probably not yet usable by others. Breaking changes are introduced on a daily basis and there is not yet an easy setup.
This is a set of tools used for processing results generated by CellProfiler for the CellPainting asssay.
The tools are designed to be used in a Jupyter Notebook and have been written in Python3.
The starting point is a Results.tsv file that contains output from a CellProfiler pipeline aggregated as medians on site level (please visit cellprofiler.org for details on how to setup and run CellProfiler pipelines).
Further documentation, including Jupyter Notebooks with example workflows, will follow.
- Switch from a categorical fingerprint to a continuous log2-fold scale
- Use 629 parameters selected based on reproducibility
- do not remove correlated parameters