rahuldhodapkar / gatsby

Tools to infer local feature dependencies in spatial transcriptomics datasets

GATSBy

Graph ATtention for Spatial Biology

Tools to infer local feature dependencies in spatial transcriptomics datasets

All code developed for use on *NIX systems with CUDA capability.

Introduction / Background

Data

Framework Overview

Usage

Environment Setup

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

Data Configuration

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.