SPIRAL v1.0

SPIRAL is a method for batch effect removing and coordinationg alignment for spatially resolved transcriptomes.

News

SPIRAL based on pyG (pytorch Geometric) framework is availabel at https://github.com/guott15/SPIRAL_pyG

Usage

SPIRAL consistis two consective modules

• SPIRAL-integraion
• Input
  feature mat: Ncell x Ngene
  edge mat: Nedge x 2
  meta mat: Ncell x 1 or Ncell x 2: batch label (necessary) or domain label (selective)
• Output
  embeddings: Ncell x zdim
  recovery gene expression: Ncell x Ngene
• SPIRAL-alignemnt
• Input
  embeddings of SPIRAL-integration: Ncell x zdim
  clusters
• Ouput
  aligned coordinates: Ncell x 2
• Demo can be obtained in Demo floder

Installing

git clone https://github.com/guott15/SPIRAL.git
cd SPIRAL
python setup.py build
python setup.py install

Note: pytorch_revgrad should be in your current path.

Data

data are stored at https://drive.google.com/drive/folders/1ujS3504u1Ge0wT3_LcCbGk_DNZut2SeK