This package contains a simulator that is able to generate multi-modal data (i.e., microscopy-like, spatial-omics-like, single-cell-sequencing-like) from a set of input parameters. Please keep in mind that currently the aim of this simulator is not to attain an higher degree of biological fidelity. Instead, the main advantage is to have a controllable tool that allows to mimic some underlying processes that govern biological data in a principled way, i.e., knowing the hidden "ground-truth" that is governing the correlations between the different modalities.
- Create your conda or venv environment:
python -m venv venv && source venv/bin/activate
- To install the package locally from GitHub, clone the repository and install the package in development mode:
pip install -e git+https://github.com/juglab/MultiOmicsCellSim.git
If you get an error regarding a missing seuptool-based build, please upgrade your pip installation.
Just pull the repository, cd into it and install with python -m pip install -e .. Again, ensure you have an updated version of pip which supports hatch and editable mode together.
- Tissue-level pictograms (WIP): Generate microscopy-like images starting from some input features at a tissue, cell and subcellular level.