scMIAC

Single-Cell Multi-modality Integration via cell type filtered Anchors using Contrastive learning

Installation

• Create a conda environment

conda create -n scMIAC python=3.8
conda activate scMIAC

• Install PyTorch according to your CUDA version

# example:
pip install torch==1.10.0+cu111 torchvision==0.11.0+cu111 torchaudio==0.10.0 -f https://download.pytorch.org/whl/torch_stable.html

• Install scMIAC

wget https://github.com/Telogen/scMIAC/archive/refs/heads/main.zip
pip install main.zip

Usage

Data preprocessing

Notes: Ensure:

• The normalized expression matrix of all genes is in .raw attribute.
• The normalized activity matrix of all genes is in .raw attribute.
• The predicted cell type labels are in .obs['pred'] attribute.

Example: https://github.com/Telogen/scMIAC/blob/main/tutorial/preprocess.ipynb

scMIAC for diagonal integration

Example: https://github.com/Telogen/scMIAC/blob/main/tutorial/demo_diagonal.ipynb

scMIAC for vertical integration

Example: https://github.com/Telogen/scMIAC/blob/main/tutorial/demo_vertical.ipynb

scMIAC for horizontal integration

Refer to: https://github.com/Telogen/scMIAC/blob/main/tutorial/demo_diagonal.ipynb

Contact

ljtian20@fudan.edu.cn