scSLAT: single cell spatial alignment tools

scSLAT package implements the SLAT (Spatial Linked Alignment Tool) model to align single cell spatial omics data.

Directory structure

.
├── scSLAT/                  # Main Python package
├── env/                     # Extra environment
├── data/                    # Data files
├── evaluation/              # SLAT evaluation pipeline
├── benchmark/               # Benchmark pipeline
├── case/                    # Case studies in paper
├── docs/                    # Documentation files
├── resource/                # Other useful resource 
├── pyproject.toml           # Python package metadata
└── README.md

Tutorial

Tutorial of scSLAT is here, if you have any question please open an issue on github

Installation

Docker

Dockerfile of scSLAT is available at env/Dockerfile. You can also pull the docker image directly from here by:

docker pull huhansan666666/slat:latest

PyPI

Note Installing scSLAT within a new conda environment is recommended.

First, we create a clean environment and install scSLAT from PyPI. We need install dependency torch before install pyg.

Warning old NVIDIA driver may raise error, please update NVIDIA driver to the latest version.

conda create -n scSLAT python=3.8 -y && conda activate scSLAT
pip install "scSLAT[torch]"
pip install "scSLAT[pyg]"

Note Some dependencies such as torch-scatter need to compile from source, which may take a long time. Please refer our solution to accelerate the install here

Development version

For development purpose, clone this repo and install:

git clone [email protected]:gao-lab/SLAT.git
cd SLAT
pip install -e ".[torch]"
pip install -e ".[pyg,dev,doc]"

Conda (Ongoing)

We plan to provide a conda package of scSLAT in the near future.

Reproduce manuscript results

1. Please follow the env/README.md to install all dependencies. Please checkout the repository to v0.2.0 before install scSLAT:
2. Download and pre-process data follow the data/README.md
3. Whole benchmark and evaluation procedure can be found in /benchmark and /evaluation, respectively.
4. Every case study is recorded in the /case directory in the form of jupyter notebook.