- Tools to analysis mFISH data, including gene panel selection from reference dataset.
- This is a python version of https://github.com/AllenInstitute/mfishtools with slight modifications
- Bootstrapping instead of subsampling
- Multiple iterations (default=100) per gene addition instead of single random seed to increase reliability across repetition
- Parallel computing using dask
- Some functions are not included yet. (e.g., fraction_correct and dendrogram_height optimization)
- This is still in active development (as of 12/10/2024)
pip install mfishtoolspy
Or
git clone https://github.com/AllenNeuralDynamics/mfishtoolspy.git
cd mfishtoolspy
pip install -e .