Tools to infer local feature dependencies in spatial transcriptomics datasets
All code developed for use on *NIX systems with CUDA capability.
The main toolset is built in python and machine learning components
are implemented on PyTorch
.
Python dependencies managed through [conda
]. After installing conda
, create an environment with:
conda create -n gatsby python=3.8
Then activate the environment with
conda activate gatsby
Raw data is not shipped with the software, and should be populated into a local data folder prior to starting a run. We provide a handy script to populate and/or check data contents against our stashed checksums.
make configure
Will run these scripts.