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