README.md

STARfinder

The processing pipeline for spatial transcriptomics data generated by STARmap-related methods.

Datasets

Following datasets are provided for testing:

1. HeLa cell culture dataset (cell-culture-3D)
2. Mouse brain tissue section dataset (tissue-2D)

Additional sources: Single Cell Portal

Usage

To create a starfinder python environment:

conda env create -f ./config/environment.yaml

Demos

Following demos are provided:

1. Sequential workflow for image processing

   • Available datasets: HeLa cell culture dataset, Mouse brain tissue section dataset
   • Software requirements: MATLAB 2023b or newer

2. Downsteam analysis

   • Available datasets: HeLa cell culture dataset, Mouse brain tissue section dataset
   • Software requirements: Python: starfinder

Workflow

Starfinder can also be used as a snakemake workflow

Notes

For Broad/WangLab user, starfinder can be executed on the UGER cluster with the provided profile.

Citation

TBA

Contact

For questions and help requests, please use the issue tracker.

License

MIT license